looks like you simply need a new stator from your readings. I will agree to disagree with the other poster about the outside of the flywheel not doing anything. Thats where the magnets are for the pick up coil, and when those rust it wont have spark, the inside of the flywheel is lined with stainless steel so it doesnt rust, it can become covered in a soot like coating but that will merely diminish the output of the lighting coils not the spark that comes from the pick up coil.
As mentioned earlier the pick up coil is bad and the only way to get one from yamaha is buy a new stator. One word of advice... buy a oem yamaha stator, dont go for the aftermarket stators, yes.. they are better priced but they dont last or even work at all so your time must be of some value to you so get a oem yamaha.
to change it is pretty easy, just remove exhaust can,remove recoil and then the 3 bolts that hold the recoil cup on( heat these up real good and quickly with a mapp gas torch to release the locktite on them so you dont strip out the heads, once those are off you remove the large nut and lockwasher. Use a steering wheel puller with 3 bolts just threaded into the flywheel the thickness of the flywheel and then it will pop it off( I use a impact gun and they pop right off). Youll then see 3 phillips head screws and 2 small allen head screws holding the pick up coil on, remove those and unplug the staotr. replace.... and it will run again!