Read up on how to do a compression ratio calculation (it's not hard at all) and check what your motor comes out with against with other 250 owners compression ratios and what a stock 250 is. If its too high then it is likely that that's the problem, otherwise check it for air leaks by doing a leak test (I think a lot of people do this every time they rebuild their engine). Detonation can cause those marks on the piston and head-look up 'two stroke detonation piston' on google images.