Anytime that I’ve had a problem with the bolts holes not lining up, I just sit the intake straight on the heads with no gaskets. If they line up better, the thickness of the gasket is about the right amount to remove. My machine shop has a tool they have made to help with the angle. If the angles are off, they need to be corrected. It is two parallel bars bolted together in a V. You lay it in the valley and square it up with the heads and set the angle. He machines the amount and correct angle and you are good to go. Had it done on several intakes and it comes out perfect.