Stuart, the mated manifolds were machined as a paired unit, but they did have a fairly significant warp before being machined, and I believe that a fair amount of material was taken off. It's entirely possible that the alignment rings are preventing good coaptation of the intake ports to the manifold. I'll try disassembling, sanding down the profile of the alignment rings about 20% and putting on a new gasket. Also will take the opportunity to put on new studs - truck has the originals.
I agree with your comment about the head, I think it's fine. I ground the intake valves at overhaul and had some hardened exhaust valves fabricated for it.
Thanks for your thoughts.
R