I would like to hope that the intake ports on the heads have been milled an appropriate amount to match the 0.050" that was taken off the decks. this is required in order to get the intake to line up properly and and bolt down.
Then if the heads are ported, you can check to see if the intakes on the heads have been enlarged to the intake gasket port size. I am sure they would have been.
Then, as Moper mentioned, you should take your intake manifold and enlarge the openings to also match the gasket ports...that will increase the flow out of the manifold into the heads.