I don't think that Yamaha will be releasing info on their new 3 banger engine for a while.
Maybe, if some of you guys know official Yamaha dealer mechanics you could ask them about the engine specs on this bikes engine (ie: timing, valving or YCC-T) they might be able to figure out where the problem is coming from.
I'm not sure if this would help but maybe those of you that actually own the bike

and that have a ticking noise could try this:
-While riding your FZ9 with high Octane fuel (91-93 RON), once you start to hear the ticking noise you should change between power modes(Standard, A and B)
Maybe the fuel mapping and timing while change between modes and it will stop or increase ticking.
I'm also kind of thinking gas doesn't have anything to do with the noise because the bike here was running on premium gas (which is like 98 RON versus 91-93 US gas, so basically race gas), so knock wouldn't be a concern.
Like RichBinAZ mentioned that if they've thinned down the casting walls inside the housing and engine as much as possible to save weight that that might have something to do with the extra noise resonance.
Does anyone know if the FZ9 has hydraulic valves or are they mechanical?
Also when you guys say that the noise is coming from the right side of the engine, is that when your sitting on it or facing it?
I'm assuming when you're sitting on it. Maybe you're hearing the camshaft gears or the oil pump which is located on the right side: