Notice the lip on the intake port, this is stock. All large port heads should have this lip. Unfortunately some heads get damaged or modified and the lip disappears--like the head on the right. This causes problems with the distance between the two heads when they are on the motor, and it makes your intake manifold too short.
Here is the solution to the problem. My dad made up a ton of intake inserts, and had a couple special ones made up. The stock one is on the left, and the special one is on the right, notice that the threads that stick out of the head are longer to compensate for the missing lip. My dad is a pretty fart smeller, or is that smart fellar? You be the judge.