A lot of times when a set of heads is machined, only the block surface is touched. This can cause the intake bolt holes to not line up properly. Material needs to be removed from the intake sealing surface of the head as well.
I just test fit my new air gap intake on my 360. I can just barely get the bolts started. The bolts cut threads into the bottom of the intake holes. The heads need to have a little material removed from the intake surface so the intake will sit a little lower.