Certainly starting to sound like a head specific problem for sure. You have a set that fits fine, so obviously the H/S do work fine on these heads, just not that particular pair. You'll be needing to do a little minor custom work it appears.

The Cranes fit standard iron heads fine, and some Edelbrocks fine, but they too need to be changed. I have spoke to Crane about this, but its not on the immediate " to do" list". H/s will make semi customs as well by moving some of the components for you, as will T&D.