I suppose it can't hurt to torque everything, but I only use a torque wrench for very critical things like head bolts. For most things I just use common sense, the bigger the bolt or nut the more muscle I use; axle nuts get way more than little 4 - 6 mm bolts.
torque specs...this has always been a sticky subject no matter what, but they are there for a reason. get your self a standard hardware torque spec guide if you don't have a manual, but that will only get you so far if you can't identify what size the hardware is for proper torque value to apply. there usually is a min-max value to hardware to go by...my rule of thumb is to stick with manufacturer specs. if you're unsure, then go direct to tech support via dealership or Yamaha.
you can find the pdf for the fz or get the Haynes manual, either will do you well. the mind set of using German torque of good n' tight isn't something you want to play with, just words of caution.