Update!
So my fabricated intake manifold was warped on the head side flange. The throttle body flange was fine, at least. Machine shop is planing the flange this week.
Hopefully once that goes in, everything should work properly. I’ve been dialing in the rest of it, and I think that basically all other systems are working properly. Assuming that it will idle properly and respond to tuning inputs I make, it should be ready to go to the tuner.
Once that’s all done, I think all that is left is getting cruise control, AC and traction control working which will be springtime tasks.