I just had this exact same set-up on my boy's 2000 YZ 250. Four allen-head set screws holding the flywheel in place, no nuts at all. If they were stripped, I would suggest drilling them out as you did, and then re-tapping a little larger later. To get the flywheel off, we bolted a 3 foot piece of hardwood (metal may have been better . . ), to the flywheel using the 2 threaded holes in its outer surface. I think these would be mounting holes for the factory removal tool. Then we re-installed the clutch basket on the crankshaft splines on the other end, and held this carefully with a chain wrench ($10. at auto supply store - Princess Auto in Canada). Then using the leverage we unscrewed the flywheel from the threaded end of the crankshaft (NO PULLING NEEDED - we originally tried this . . . ). Don't lose the Woodruff? half-moon locking key that holds the flywheel in the correct place on the crankshaft. The final disassembly required setting the left side crank case up on wooden blocks, placing a drift (or something hard, and about 1/8" in diameter) in the centre of the threaded end of the crankshaft, and whacking her really hard. This released the crankshaft from its left side bearing. Now a question >>> does anybody know how we can split the crank shaft weights to get at the connecting rod bearing?? Thanks.