Intake won't bolt on!

If the bolt holes are not lined up, then the ports aren't lined up either! I've seen people take the easy way out and open up the bolt holes to make clearance for the bolts, but that just isn't right.

Eyeball the "intake hole/intake bolt holes in the head" alignment with the gasket, then without. If the alignment is good without the gasket, mill the intake sides of the manifold the thickness of the intake gaskets. If the alignment is only "1/2 way there" without the gasket, mill the manifold twice the thickness of the gasket.

This may not be completely accurate, but it's the easiest way to fix the issue correctly. The drawback is that the intake will only be good for that block/head combo. Usually the intake side of the head is milled for manifold alignment so other new intakes can be swapped with minimal or no more issues.