Experts and Know-it-alls welcome..

IF the heads had the combustion side cleaned up to make them flat, or the chambers smaller to raise the compression, the face the intake bolts to may not be at the same angle, so the face of the intake may not lay flat against it. you'll find out the hard way when it sucks oil into the intake and cylinders
Or the block was decked.. did the intake go to the machine shop w/ the heads? If they milled the heads, should a cut the bottom of the intake