I have a 06 raptor 350 and the woodruff key keeps shearing. I have make custom ones to fit,got a new flywheel, looked over and rebuild almost the entire top end. I even used lapping compound to get a tight fit for the flywheel. I finally thought I fixed it and it was running really good for about 5 min. Then it started sputtering then it backfired and emidiatly died and the key sheared again. And ideas of y it keeps shearing.

 

Don't know the raptor model at all, but you seem to have done everything. Are you sure that both tapers were the uniform grey you get with a lapped in finish? You sometimes get a bur at the edge of the keyway which stops it from lapping properly. Only other thing I can think of is the holding nut/bolt bottoming on it's threads before it tightens on the flywheel, so not gripping it properly. I assume you have double checked that you are setting it to the correct torque. Strange too that it ran for a while, as the most strain on the flywheel taper is when starting, as electric starter power goes through flywheel to crankshaft then.

 

Would it make sense if the crank was worped? The guy we got if from tried to weld the key in.

 

Like I wrote above, uniform grey all the way round where the tapers meet, means the tapers are correct, ensure there isn't a step behind the taper as the flywheel has to slide a little past the ground area as it tightens. If tapers are right, I can;t see a distorted crank affecting the flywheel. My bet is still on whatever is supposed to tighten the flywheel onto the taper, bottoming out before it does so.