Milling the stock sheave may be an issue. Any spring or weight calibrations should be fine. If you switch out the primary weights for 18 gram weights, you will have the same calibration as the Grizzly which should be more than enough for most "normal" sized tires and riding. People mill sheaves when they need to pull really big tires in really muddy bogs. Shimming is the poor mans way to achieve what cutting a sheave will do. If you really want a cut sheave, I would go with this outfit. They give you a milled out sheave, weights and spring. You get everything in one package and you can keep your stock sheave stock and in the tool box. A setup like this shouldn't have any bearing on warrantee IMO. Again, unless your trying to accomplish something in particular, I'd try some Grizzly weights first, then go from there. I'm sure you would get a wheelie machine and save a bit of coin.
http://www.jbsperformance.com/yamaha/clutching
http://www.jbsperformance.com/yamaha/clutching