Intake manifold Not seating properly (?)

Locomotion said

While you're at it, with the intake on the long block, see if the bolt holes line up.If they line up perfectly without gaskets, then they won't when you add gaskets and you'll need to mill the thickness of the gasket off of the heads or the intake. Any other misalignment differences you'll have to estimate milling accordingly.

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This can be misleading. The factory used thin metal like shim stock for a gasket so with or without those would hardly make a noticeable differencein bolt hole alignment.
( Crush allowance for shim stock is only .003 )
Aftermarket gaskets are typically a composite ( I use felpro print-a-seal ) that is several times thicker than the OEM. Even so, if the heads haven't been milled the bolts will go.
Torqueing the bolts to spec will crush a composite gasket considerably more than the metal. ( crush allowance for composite gaskets varies with makeup, application, and torque spec ).