HELP intake bolt holes not aligning

have your intake cut an amount equal to or just slightly less than the thickness of the gaskets.....done all the time.
YES, usually it is better to cut the cylinder head intake gasket surface rather than the intake manifold. But either will work. Since your intake fits with no gasket Burch is correct suggesting to cut the intake surface about equal to the intake gasket thickness. Should not need to cut the front/rear intake surfaces that seal to the block if RTV sealant is used rather than the cork gaskets.

With the intake cut, then the gaskets between the intake and heads can be used.