After riding it last night, my issue still persists after cleaning the sensors. My bike is really new still. Less than 3k miles.

Not sure what is causing it. I have a stutter/surging with around 1/4 throttle and cruising. I notice that idle seems slightly uneven. Very light bouncing of the rpms. Bike is fine WOT or normal accelerating.

 

can you adjust the tps and the aps doing the mode button ?as in turn it alittle mode button no work back up alittle mode button works , now should be good method

 

Thank you!!!! I've had this issue for a while now and hope this is finally the fix! I kept going at it over and over again and this problem kept rearing it's ugly head.

 

I've noticed if you drag the brakes when the stuttering happens, the stuttering goes away. Is this problem possibly related to an engine load sensor or the ECU reading/calculating engine load?

 

If it's the same stutter i have (mini backfires at steady throttle, low rpms), going up a steep hill (loading the engine) makes it go away. Haven't gotten around to do a TB sync or checking my connections yet. I've heard other bikes on youtube to the same thing. It's just an annoyance, but pretty annoying


What i know so for:
- Bike is a bit rich. Running Akra TI, o2 sensor eliminated and a 2017 flashtune flash. Axle blocks and nut is going brown, and people tell me they smell gas behind my bike when i give it a bit of throttle.
- I get gurgling / minipops for about a second on decel when crossing the 4k rpm border after a 1/4 turn or more acceleration.
- I had this issue before adding the block off plates.
- I didn't notice this issue before the exhaust and flash. Did both at once, but I've ridden in lots of rain and keep my bike very clean. Might not have not noticed it with the stock exhaust due to how silent it is.
- Plugs were replaced last service, no change.
- The Akra exhaust has a built in leak in the collector that akrapovic tells me is normal, and I've checked other Akra headers and they also have the same gaps to let air in.

See the video below for what I'm experiecing. It's extreme at the 40 second mark.

 

Ifan,

How many miles do you have and what year is your FZ?

Before listening to the video, i thought its a classic air leak at the header gasket area.

No pun intended, but that sound is baffling to me. It doesn't sound exhaust related. Usual decel popping sounds completely different than your issue, its weird. Its almost sounds like 2 things rubbing together when the engine is at load, like when you say at 4k rpm's.

Id suggest looking elsewhere for the issue. Any other sounds or vibrations going on? Hows the chain slack (dont think its this, but just asking).

The gas smell, do you ever try to get every last drop in the tank when you fill up, or do you stop before seeing liquid gasoline?

Others may have better idea's.....

 

23000 km, 2016 EU MT09 with TC and ABS. It started after mounting the exhaust and flashing it a couple of years ago, or maybe it was there before that but you couldn't hear it with the stock exhaust. The aftermarket exhaust has been off and mounted again, with new gaskets as well, no difference.

Nothing is rubbing, the sound is definitely from the exhaust. The sound is a bit more muted irl compared to the video. It only happens at steady / almost closed throttle in the 3-4000rpm range. It doesn't happen when the bike is cold and doesn't happen with load (going up a steep hill).

 

Ever get any error codes?

That is an odd one. If I think of anything, ill respond but i am stumped.

In the future, its best to do one mod at a time, that way if problems arise, you know what caused it. Just speaking from experience here.

 

Had the check engine light come on after installing the ECU after the flash. The mechanic said about all the codes were active. Got it reset and only have a few recurring ones, but no CEL. The codes are C1555, P1EF5, P1EF0 that seem normal as I've seen them on other MT09s.
I think I've found the key to reference the OBD2 fault code with the fault numbers in the service manual. I asked the dealer to get the codes with the yamaha numbers on it for me, and i correlated that to the OBD numbers. It's just a hex to decimal conversion of the two last digits in the fault code.

P1EF0, F0 to dec= 240, means o2 sensor fault, which is reasonable as it's gone and disabled in the flash. I've also added an o2 eliminator dongle, just a couple of resistors.
P1EF5, powertrain. F5 to dec= 245, means engine stop detected. This one is a bit more generic and might be a plethora of things, and the service manual says it can be occasionally be thrown under normal operation.
C1555, chassis, 55 to dec = 85. Haven't been able to find this one in the manual, but my guess is it's just the sidestand switch kicking in or something.

 

So, I've been trying to figure out my issue all season. I've adjusted the TB Sync twice now. I've cleaned the sensors with electrical cleaner.

I've been communicating with VcycleNut a ton through email. He thinks my issue is TPS related and I agree with him, but I can't tell what is causing it.

This past week when I did my second TB Sync this season (thinking I messed it up the first time) when I went for my first ride, I thought I solved my problem. My issue was completely gone. I chalked it up to either I fixed a vacuum leak, or the TB Sync did it.

Then, the following day I rode again all day and the bike was right back to where it started. 1/4 to 1/3 throttle is stuttering like crazy.

Here's a short video I took showing the symptom:

You can hear the issue present itself in first gear around :25 seconds and again around 1:20.

When you hear the rpms bouncing, I'm holding the throttle completely still at around a quarter throttle.

New video by Jon Dagata

photos.app.goo.gl

Does anyone know how to check the TPS data on a 2017? As far as I can tell form the service manual, there isn't a diagnostic mode anymore so you need a data reader. I have the OBD2 converter cable as well as an OBD2 bluetooth adapter and the Torque app.

Attached are two screenshots from Torque. One is 0 throttle, the other is 100% throttle. The three numbers in Torque are "absolute throttle position b", "relative throttle position", and "Throttle Position (manifold)".

I have no idea how to tell if these numbers are normal or not.

Hoping someone here can guide me.

EDIT:

Also, when I scan for error codes, I have no red or yellow codes, but a bunch of grey ones. I'm not sure what they all mean.When I clear them, a few come back, but they are grey so I don't know if they are active or what. (Screenshot of an example is attached)

 

Some additional screenshots I grabbed tonight. I saw that "Pedal position D", "Pedal position E", and "Relative Pedal position" all were effected by changes in throttle input.

So attached is a screenshot of 0 throttle and 100% throttle for each of these 3 numbers.

These numbers seem "closer" to what the service manual states as far as TPS readings, but I'm not sure this is representative of the same data diagnostic mode 01 for TPS provides.

It is interesting that full throttle doesn't reach 100 though. Maybe someone will know if this is a problem or not.

 

It is interesting that full throttle doesn't reach 100 though. Maybe someone will know if this is a problem or not.

Haven't checked my TPS values, but my stutter is exactly at steady throttle or a very slow decel, basically in the no load / barely any load zone to the engine. No RPM bouncing for me, just popping / faffing in the closed loop rpm area at those specific throttle inputs.
The TPS values might look weird due to the throttle maps. On my 690 that i can tune at home, the TPS value only goes to 15% or something like that while the engine is off because of the throttle map isn't linear (current rpm combined with throttle position).

I remember an old thread here with someone with a similar issue to yours. He ended up changing one of the coil packs and that solved it for him. Might be worth a shot, and move it around across every cylinder until you find the culprit.

If you have a laser temp gun, quickly shut off the engine after holding stutter for a while and measure the temp on the different headers. If one is really lower or higher than the others you might atleast know which cylinder is having the issue. Expect the middle cylinder to be a little bit hotter just because it's in the middle.

Another possible cause might be clogged injector / fuel filter. Heard of lots of weird gremlins like this caused by such.

Oh - and that amount of codes isn't normal afaik. I've done scans on three MTs and i usually see P1EF0 P1EF5 and C1555, and maybe one or two more.
Convert the last two HEX numbers to decimal get the corresponding code in the service manual. This seems to work on most powertrain codes, but i can't find them all in the manual.
Example: P1EF0, take F0, convert to dec = 240.

Clear the codes and see which ones returns. If the MAP, TPS and air intake sensor codes all return i might suspect an electrical gremlin or possible faulty ECU.

 

I read through the thread, I guess to fast what was the solution?

 

No resolution yet. Lots and lots of potential causes and things to test. For me at least.

 

Update for myself:

After more testing and confusion. I sent my ECU back to Vcyclenut to be returned to stock. I'm then going to reinstall my o2 sensor and compare a video I took of a cold start right before I packed up my ECU to be sent out. Then, if the symptoms go away, i'll know I had an issue with the tune. I'm going to give Ivans tune a shot after this.

Vcyclenut believes I have some other electrical issue that has yet to be discovered. The dealership I bought the bike from said my bike was running lean and it was the tune. So I don't know. This will at least eliminate the tune if it isn't, and will confirm it's the tune if it is.

This is my video to compare against that I took literally before removing the ECU:

New video by Jon Dagata

photos.app.goo.gl

?‍♂

EDIT:

Also, one thing i'm wondering is if maybe a coil is going bad and I have weak spark under light load and idle. But when I checked header pipe temps, they seemed even. So i'm not sure.

 

I love my bike, but this year it developed a problem that ruined my entire season.

Symptoms:
My 2014 FZ-09 has 30 000km on it and started stuttering while cruising around 30% throttle. It was getting worse as time went on. The stutter was becoming more frequent, under more riding conditions and was becoming violent. The bike was also starting on the 3rd or 4th pull instead of the normal 1st pull. It got so bad that is was happening in low speed situations. Once, it happened in the middle of a busy intersection during a left hand turn... only my angel and willpower kept me up. Disconnecting the battery or unplugging the ECU would improve the situation for a while, but after 50 km it was back.

The process:
I asked my Yamaha dealer to look into it during my maintenance service and they said it was bad gas (which ticked me off). Later they told me it was plugs, (which I had changed the day before myself). So I started cruising the forums to find a solution. I changed the air filter to a K&N and did the plugs. Then I did a reflash through VcycleNut. It didn't fix the problem. Then I replaced the injectors and tightened the throttle cable. While these all improved the bike, they didn't fix the underlying problem.

The Solution:
Finally, I decided to check all of my electrical connections. When I checked the connectors for the Accelerator and Throttle Position Sensors, I found condensation inside. I cleaned them out with electrical contact cleaner, let them dry and put it all back together. Low and behold, no stutter, jerking or hiccups. On top of that, 150km on, the bike is running smoother and starts 1st pull. My guess is that the APS and TPS must have been sending bad readings to both the throttle actuator and ecu. The actuator was opening and closing according to bad signals and the O2 sensor was reading rich as a result. The ecu was probably leaning the bike out based on the O2 data. Probably why it got better when I disconnected the battery. As the emissions data is rewritten in the ECU, the bike is returning to its normal fueling. Unfortunately it took the entire riding season to discover.

Recap:
Clean the electrical connectors for the APS and TPS to fix the problem. I plan on doing it every spring.

P.S. The VcycleNut flash greatly improved the bike. They have excellent customer service and maintain prompt correspondence throughout the process, it is also a cheaper alternative to throttle commanders and O2 deletes. Also, the manual states 1/4" play in the cable, that is WAY too much. Tighten to where its comfortable. (No wonder my right hand was always tired an numb.)

hello! this is very useful. i just got a 2017 fz09 demo bike from a dealership and have been encountering some strange issues. I would like to try and clean the connectors as you did but i have absolutely no idea where i would find them, where exactly are these connectors located? thankyou.

 

See post #13 on page #1 of this thread...you will have to remove the tank and air filter box to properly get to them ..

 

Just replaced the APS and TPS and also cleaned the throttle bodies. Jerkiness/surging/stutter is gone!
My guess is that either the APS or TPS looked like @shamrock 's mentioned in post #10. Before I did this I went into the DIAG menu and "tested" the APS and TPS and they both hit all the values when you opened the throttle slowly so I assumed they were fine. After going to a local bike mechanic he test rode it and told me it seemed like a TPS problem and that's why I decided to just go ahead and buy both sensors and replace them myself. It ended up being just over $200 shipped from partzilla. Glad to put this behind me finally.

 

Hmmmmmmm. Did you test it and figure out which one specifically it was? The TPS or APS?

Can you link me to the part? I can't seem to find it.

 

Items #11 &13 ... https://www.shopyamaha.com/parts-ca...=Road&nw=yamaha-motor-company&dealernumber=#/Yamaha/FZ09_-_FZ09FS_-_2015/INTAKE

 

Just ordered a replacement tps and aps.

Reinstalled my stock flashed ECU and the problem is still there. That rules out any tune issues. (as I expected)

Have a replacement battery on it's way as well.

I'm taking a video of the bike after each change and comparing them.

 

Parts should be here tomorrow, so I should know this weekend if this solves my problem!

 

Replacing TPS and APS solved my issue. I may need to adjust the throttle position sensor angle a tad, or my bike doesn't like the Lextek exhaust with the stock tune.

When I first start it, it idles slightly low and stalls if I give it throttle. This is only when it is cold. When it warms up it seems to be running great.

Is there a way to read the TPS/APS angle without using a Yamaha diagnostic tool on a 2017? i have the obd2 cable and reader. I use Torque, but I don't know how to read the TPS angle like the Yamaha scan tool.

 

Is there a way to read the TPS/APS angle without using a Yamaha diagnostic tool on a 2017? i have the obd2 cable and reader. I use Torque, but I don't know how to read the TPS angle like the Yamaha scan tool.

Did you ever get any answer to this?
I recently purchased new APS and TPS sensors and would like to know if I can replace the old ones without any diagnostic tools?

 

Same issue here ! Someone had a diy for change the aps and tps ?? I bought it use on ebay from a 2016 that was running great . Do i had to go to my dealer to syncronize aps.and tps ??

 

So my FZ started sputtering again in the last week. Real jerky at cruise speed between 4000-5000 rpm. Piss me off. The winter of 18/19 I tried numerous possible fixes and in the spring of 2019 it ran great.

I replaced the Power Commander and then removed it for an updated ECU time. Played with chain tension and cleaned the APS and TPS connectors.

But wasn’t sure which one actually fixed the issue. So this week I have been trying one thing at a time. Started with chain tension. Didn’t make much difference.

So yesterday I removed the gas tank and airbox to get to the sensors. Blew them out, sprayed in contact cleaner, blew them out and added dielectric grease. Reassembled and took it for a test ride. Smooth as butter!

A week ago I drove the bike in rain!

Crazy that these connectors aren’t sealed from moisture.

 

New tps and aps ! I got a new bike my issue is solved !!!

 

I love my bike, but this year it developed a problem that ruined my entire season.

Symptoms:
My 2014 FZ-09 has 30 000km on it and started stuttering while cruising around 30% throttle. It was getting worse as time went on. The stutter was becoming more frequent, under more riding conditions and was becoming violent. The bike was also starting on the 3rd or 4th pull instead of the normal 1st pull. It got so bad that is was happening in low speed situations. Once, it happened in the middle of a busy intersection during a left hand turn... only my angel and willpower kept me up. Disconnecting the battery or unplugging the ECU would improve the situation for a while, but after 50 km it was back.

The process:
I asked my Yamaha dealer to look into it during my maintenance service and they said it was bad gas (which ticked me off). Later they told me it was plugs, (which I had changed the day before myself). So I started cruising the forums to find a solution. I changed the air filter to a K&N and did the plugs. Then I did a reflash through VcycleNut. It didn't fix the problem. Then I replaced the injectors and tightened the throttle cable. While these all improved the bike, they didn't fix the underlying problem.

The Solution:
Finally, I decided to check all of my electrical connections. When I checked the connectors for the Accelerator and Throttle Position Sensors, I found condensation inside. I cleaned them out with electrical contact cleaner, let them dry and put it all back together. Low and behold, no stutter, jerking or hiccups. On top of that, 150km on, the bike is running smoother and starts 1st pull. My guess is that the APS and TPS must have been sending bad readings to both the throttle actuator and ecu. The actuator was opening and closing according to bad signals and the O2 sensor was reading rich as a result. The ecu was probably leaning the bike out based on the O2 data. Probably why it got better when I disconnected the battery. As the emissions data is rewritten in the ECU, the bike is returning to its normal fueling. Unfortunately it took the entire riding season to discover.

Recap:
Clean the electrical connectors for the APS and TPS to fix the problem. I plan on doing it every spring.

P.S. The VcycleNut flash greatly improved the bike. They have excellent customer service and maintain prompt correspondence throughout the process, it is also a cheaper alternative to throttle commanders and O2 deletes. Also, the manual states 1/4" play in the cable, that is WAY too much. Tighten to where its comfortable. (No wonder my right hand was always tired an numb.)

I love my bike, but this year it developed a problem that ruined my entire season.

Symptoms:
My 2014 FZ-09 has 30 000km on it and started stuttering while cruising around 30% throttle. It was getting worse as time went on. The stutter was becoming more frequent, under more riding conditions and was becoming violent. The bike was also starting on the 3rd or 4th pull instead of the normal 1st pull. It got so bad that is was happening in low speed situations. Once, it happened in the middle of a busy intersection during a left hand turn... only my angel and willpower kept me up. Disconnecting the battery or unplugging the ECU would improve the situation for a while, but after 50 km it was back.

The process:
I asked my Yamaha dealer to look into it during my maintenance service and they said it was bad gas (which ticked me off). Later they told me it was plugs, (which I had changed the day before myself). So I started cruising the forums to find a solution. I changed the air filter to a K&N and did the plugs. Then I did a reflash through VcycleNut. It didn't fix the problem. Then I replaced the injectors and tightened the throttle cable. While these all improved the bike, they didn't fix the underlying problem.

The Solution:
Finally, I decided to check all of my electrical connections. When I checked the connectors for the Accelerator and Throttle Position Sensors, I found condensation inside. I cleaned them out with electrical contact cleaner, let them dry and put it all back together. Low and behold, no stutter, jerking or hiccups. On top of that, 150km on, the bike is running smoother and starts 1st pull. My guess is that the APS and TPS must have been sending bad readings to both the throttle actuator and ecu. The actuator was opening and closing according to bad signals and the O2 sensor was reading rich as a result. The ecu was probably leaning the bike out based on the O2 data. Probably why it got better when I disconnected the battery. As the emissions data is rewritten in the ECU, the bike is returning to its normal fueling. Unfortunately it took the entire riding season to discover.

Recap:
Clean the electrical connectors for the APS and TPS to fix the problem. I plan on doing it every spring.

P.S. The VcycleNut flash greatly improved the bike. They have excellent customer service and maintain prompt correspondence throughout the process, it is also a cheaper alternative to throttle commanders and O2 deletes. Also, the manual states 1/4" play in the cable, that is WAY too much. Tighten to where its comfortable. (No wonder my right hand was always tired an numb.)

I love my bike, but this year it developed a problem that ruined my entire season.

Symptoms:
My 2014 FZ-09 has 30 000km on it and started stuttering while cruising around 30% throttle. It was getting worse as time went on. The stutter was becoming more frequent, under more riding conditions and was becoming violent. The bike was also starting on the 3rd or 4th pull instead of the normal 1st pull. It got so bad that is was happening in low speed situations. Once, it happened in the middle of a busy intersection during a left hand turn... only my angel and willpower kept me up. Disconnecting the battery or unplugging the ECU would improve the situation for a while, but after 50 km it was back.

The process:
I asked my Yamaha dealer to look into it during my maintenance service and they said it was bad gas (which ticked me off). Later they told me it was plugs, (which I had changed the day before myself). So I started cruising the forums to find a solution. I changed the air filter to a K&N and did the plugs. Then I did a reflash through VcycleNut. It didn't fix the problem. Then I replaced the injectors and tightened the throttle cable. While these all improved the bike, they didn't fix the underlying problem.

The Solution:
Finally, I decided to check all of my electrical connections. When I checked the connectors for the Accelerator and Throttle Position Sensors, I found condensation inside. I cleaned them out with electrical contact cleaner, let them dry and put it all back together. Low and behold, no stutter, jerking or hiccups. On top of that, 150km on, the bike is running smoother and starts 1st pull. My guess is that the APS and TPS must have been sending bad readings to both the throttle actuator and ecu. The actuator was opening and closing according to bad signals and the O2 sensor was reading rich as a result. The ecu was probably leaning the bike out based on the O2 data. Probably why it got better when I disconnected the battery. As the emissions data is rewritten in the ECU, the bike is returning to its normal fueling. Unfortunately it took the entire riding season to discover.

Recap:
Clean the electrical connectors for the APS and TPS to fix the problem. I plan on doing it every spring.

P.S. The VcycleNut flash greatly improved the bike. They have excellent customer service and maintain prompt correspondence throughout the process, it is also a cheaper alternative to throttle commanders and O2 deletes. Also, the manual states 1/4" play in the cable, that is WAY too much. Tighten to where its comfortable. (No wonder my right hand was always tired an numb.)

I love my bike, but this year it developed a problem that ruined my entire season.

Symptoms:
My 2014 FZ-09 has 30 000km on it and started stuttering while cruising around 30% throttle. It was getting worse as time went on. The stutter was becoming more frequent, under more riding conditions and was becoming violent. The bike was also starting on the 3rd or 4th pull instead of the normal 1st pull. It got so bad that is was happening in low speed situations. Once, it happened in the middle of a busy intersection during a left hand turn... only my angel and willpower kept me up. Disconnecting the battery or unplugging the ECU would improve the situation for a while, but after 50 km it was back.

The process:
I asked my Yamaha dealer to look into it during my maintenance service and they said it was bad gas (which ticked me off). Later they told me it was plugs, (which I had changed the day before myself). So I started cruising the forums to find a solution. I changed the air filter to a K&N and did the plugs. Then I did a reflash through VcycleNut. It didn't fix the problem. Then I replaced the injectors and tightened the throttle cable. While these all improved the bike, they didn't fix the underlying problem.

The Solution:
Finally, I decided to check all of my electrical connections. When I checked the connectors for the Accelerator and Throttle Position Sensors, I found condensation inside. I cleaned them out with electrical contact cleaner, let them dry and put it all back together. Low and behold, no stutter, jerking or hiccups. On top of that, 150km on, the bike is running smoother and starts 1st pull. My guess is that the APS and TPS must have been sending bad readings to both the throttle actuator and ecu. The actuator was opening and closing according to bad signals and the O2 sensor was reading rich as a result. The ecu was probably leaning the bike out based on the O2 data. Probably why it got better when I disconnected the battery. As the emissions data is rewritten in the ECU, the bike is returning to its normal fueling. Unfortunately it took the entire riding season to discover.

Recap:
Clean the electrical connectors for the APS and TPS to fix the problem. I plan on doing it every spring.

P.S. The VcycleNut flash greatly improved the bike. They have excellent customer service and maintain prompt correspondence throughout the process, it is also a cheaper alternative to throttle commanders and O2 deletes. Also, the manual states 1/4" play in the cable, that is WAY too much. Tighten to where its comfortable. (No wonder my right hand was always tired an numb.)

Tim, thanks for post.
Very similar issue on 2014 MT09 27,000miles - change plugs, air filter, ecu flash, balanced carb valves. Your cleaning APS & TPS connections seems to have cleared the sputtering. Will now clean regularly and use some dielectic grease. Thanks, really appreciate.

 

Me too would like to thanks Tim. Same issues on my 09Sp 2021, from more than 4 month. Done everything without any solutions... at last i read this topic, unplugged the Tps, cleaned with air, sprayed with contact cleaner, and isolated with dielectric grease. Stuttering are disappeared.

Inviato dal mio SM-A528B utilizzando Tapatalk

 

Me too would like to thanks Tim. Same issues on my 09Sp 2021, from more than 4 month. Done everything without any solutions... at last i read this topic, unplugged the Tps, cleaned with air, sprayed with contact cleaner, and isolated with dielectric grease. Stuttering are disappeared.

Inviato dal mio SM-A528B utilizzando Tapatalk

Where is the aps sensor located on your bike; at the throttle housing. I need a picture of this part, or part number.. ty

 

When you clean the tps. Are you just disconnecting the connector and cleaning the contacts of the plugs or actually opening the sensor up and cleaning interior parts within in it
Thanks in advance all

 

How are you guys removing the tps it has two hex bit screws on each side and is too close to the frame to reach a driver or anything else in there

 

I love my bike, but this year it developed a problem that ruined my entire season.

Symptoms:
My 2014 FZ-09 has 30 000km on it and started stuttering while cruising around 30% throttle. It was getting worse as time went on. The stutter was becoming more frequent, under more riding conditions and was becoming violent. The bike was also starting on the 3rd or 4th pull instead of the normal 1st pull. It got so bad that is was happening in low speed situations. Once, it happened in the middle of a busy intersection during a left hand turn... only my angel and willpower kept me up. Disconnecting the battery or unplugging the ECU would improve the situation for a while, but after 50 km it was back.

The process:
I asked my Yamaha dealer to look into it during my maintenance service and they said it was bad gas (which ticked me off). Later they told me it was plugs, (which I had changed the day before myself). So I started cruising the forums to find a solution. I changed the air filter to a K&N and did the plugs. Then I did a reflash through VcycleNut. It didn't fix the problem. Then I replaced the injectors and tightened the throttle cable. While these all improved the bike, they didn't fix the underlying problem.

The Solution:
Finally, I decided to check all of my electrical connections. When I checked the connectors for the Accelerator and Throttle Position Sensors, I found condensation inside. I cleaned them out with electrical contact cleaner, let them dry and put it all back together. Low and behold, no stutter, jerking or hiccups. On top of that, 150km on, the bike is running smoother and starts 1st pull. My guess is that the APS and TPS must have been sending bad readings to both the throttle actuator and ecu. The actuator was opening and closing according to bad signals and the O2 sensor was reading rich as a result. The ecu was probably leaning the bike out based on the O2 data. Probably why it got better when I disconnected the battery. As the emissions data is rewritten in the ECU, the bike is returning to its normal fueling. Unfortunately it took the entire riding season to discover.

Recap:
Clean the electrical connectors for the APS and TPS to fix the problem. I plan on doing it every spring.

P.S. The VcycleNut flash greatly improved the bike. They have excellent customer service and maintain prompt correspondence throughout the process, it is also a cheaper alternative to throttle commanders and O2 deletes. Also, the manual states 1/4" play in the cable, that is WAY too much. Tighten to where its comfortable. (No wonder my right hand was always tired an numb.)

Great info I will attempt this at weekend thanks for the info,I had my ecu flashes and for a while it was smooth all the way and power was much better,but this may solve the low speed 3k to 4k stuttering that only happens when trying to cruise along but not when opening the taps,if you whack the throttle open it's fine just don't like the small openings and the other fix I seen about going into diagnostic isn't an option on the 2018 tracer,the older ones you can hold 2 buttons on and turn the ignition on to access diagnostic to make adjustments but not 2018.