Okay.

As best I understand, there shouldn't be any perceptible gap between the intake manifold and the cylinder head
anywhere on the intake port flange.

A really rough test--if you lay the manifold on the heads without gaskets, and can get (just for instance) a .004" or so feeler gauge between the parts, it should be corrected, the gasket probably isn't going to take up the difference.

If .004 won't fit, gently try .002......you don't want any gaps