Yes, I do now believe that this mismatch and my failure to recognize it led to my cross threading the bolts. And also that eyeballing the tapping and relying on tap to follow the hole was not sufficiently accurate.
They are so close and the way they install pulls them down due to the bolt angles. It's the final resting place that matters. Everything was machined to align ports. Machinist used a 1200 gasket set in the process. Can't swear to it, but pretty sure that I installed the heads and intake as a set, which I suspect may be part of my issue. I did have to rap on it with a rubber mallet to break it loose.
So today I'm stripping the plenum and injectors to take a look at port alignment. Have an angle gauge on the way and an old iron head to measure and compare bolt angles. Try and find engineering diagram with factory spec and see what I can find, make or have made to use as a drill/tap guide.