I think the problem your thinking off is actually in the older heads becuase they have a different angle.
They do have the smaller head bolts @ 5/16's rather than 3/8's.
Perhaps you'll need to enlarge the bolt holes in the intake.
Hey RumbleFish, thanks for the reply. Are all the holes at the wrong angle or just some? If some,do you know which ones? Is the actual manifold-to-head face the same angle?