BEST. i am in a machine trades class for high school so if u could go more in depth on a way i could fix this it would be a big help for me and my wallet!!!
This is the type of die you want (in the right size and thread pitch M12x1.25???):
Note the adjustment screw just visible in split. Screw it in just enough so you can thread the die over the crank threads by hand, then back that screw off just enough to clean up the threads. You do not want to cut deep, so go careful here. Use cutting oil of course.
If you were able to clean the threads up without touching the bottom of the thread, you may get by with just a new nut. With the crank thread crests damaged this arrangement is still weak so retorque carefully. Remember, oil or locktite lubes the threads (which is good) so you want to run to the low side of the torque spec.
If the die cuts into the root of the crank thread you pretty much have no choice but need and undersized nut. Two ways to do this:
1) Start with an undersized nut. I believe it has to be 14mm or 9/16" to fit in the hole anyway, so a NF or NC3/8 nut will do. I believe the crank is M12 x 1.25? So drill or bore the nut 10.75mm (or smaller) and cut the thread to fit the crank. Since you don't want to take the nut out of the lathe and the engine is too awkward to try in the nut, thread a bolt or stud with your adjusted down die and use it to try in the nut.
2) Buy a new nut from Yamaha,
And and squeeze it in a vice, like where these dimples are:
(this is a lock nut and the dimple is a punch mark to tighten the thread)
Or flattened like this factory made locknut:
Then CAREFULLY reassemble your flywheel. You might want to write a note on the flywheel or inside the cover in case you sell of forget what you did.