Something is out of whack with your parts.
Maybe a stack up of factory tolerances, I do know for a fact I have an un-touched 78 318 and changed to to a LD4B intake and with the standard blue fel-pro intake gaskets the bolts were a bear to get in.
With the shim intake gaskets the bolts would slide right in.
No machine work on the engine, bought the truck of the original owner, the engine had so much grease on it from leaky valve covers, when I pressure washed it the core plugs started leaking antifreeeze.
Engine #2 74 318 I tore down, J heads milled around .010" for flatness the 1008 head gaskets and standard intake gaskets the bolts went right in on a Victor 340 manifold.
