Ranger,
Not being familiar with the GMC, I will assume it is similar to the Chevy six. It sounds like your manifolds were not surfaced or assembled properly.
Both manifolds should have been machined together, as an assembled unit, then installed loosely bolted together before a final tightening.
If lots of material was removed during surfacing, the alignment rings might now be too wide. This could hold the intake off the head.
A freshly machined combination intake/exhaust with properly fitting alignment rings should fit perfectly flat on the head when installed correctly.
I don't think a head could ever warp on the axis that would effect sealing of the intake manifold and still have the engine run.
Stuart
