When i found that the bolt holes were too small, i did systematically go around and check all the other holes and opened them up as needed.
I am kicking myself for not doing this so thoroughly in the first place, but when you pay an engine builder to make a gasket for you as well as do the machine work i would think it should be done so it works.
Maybe i should have listened to my physics teacher when she said never assume anything, until you prove it.