I would take the bolt into a nut and bolt store, check the phone book, (not home depot, you can try but not much luck there) what you have is a pan head, you want a bugel head or even a countersunk head. this will lower the profiel and alow it to sit down flush.
the other problem here is this has already been done, and ther is no telling how much stress has been applied to the mobo, you yourself stated that if you put the case screws back in place it bends the board out of shape. that is what causes the rrod under normal conditions, so if you or the last owner bent the board, even slightly, its over, try and get your money back, resale it.