I have a Clymer manual '93-'96. Haven't found anything on line yet. Sorry for the delay getting back.
There is a woodruff key on the crank to align the flywheel. You need to secure the teeth of the flywheel gear before attaching the puller. Remove the center bolt. Book says the tools to secure the gear from turning and the puller are Yamaha tools, but I guess any puller will do. Locking up the teeth on the flywheel might be a problem. When you set up the puller and put it under load, you may have to hit the center bolt of the puller while it's under load. Do not hit the flywheel. When it pops loose, you can remove the idler gear/bendix. While the flywheel is off, inspect for metal particles or flash that might have accumulated on the magnets and remove anything. The bendix may have self-destructed in there.
I would have Yamaha inspect the flywheel for cracks, teeth and electrics, because the stator and pulser are inside the flywheel.
When you reinstall the flywheel, replace the woodruff key, wipe idler gear/bendix w/grease, position flywheel with the key slot, oil the bolt and washer and tighten to 51 ft/lbs torque.