HELP intake bolt holes not aligning

As others have said, remove any block pegs in the front & rear manifold gasket areas. Toss the cork/foam end gaskets. Use RTV. Trial fit the intake without any gaskets. If the holes line up perfectly, on both sides, mill the intake surfaces .005-.010 less than the gasket is thick. (Make up for compression.) You can guesstimate any additional difference - If the intake holes are higher, mill approx. that much more off the intake, or less if they are lower without any gaskets.

That's what I did several years ago when I found that my "EX" engine builder wallowed out the intake holes to fit instead of milling the intake side of the heads.