I think a good first step might be to disconnect power to the ECM (disconnect battery entirely) and let the ECU clear, then see what happens when you reconnect. This would clear out the stored learn trims, would it not?

Concur your problem is likely to be mechanical, not ECM. You're running a GM motor with a GM ECM. They WILL play nicely together, as has been exhibited thousands of times with enthusiast builds. It's time to start with the fundamentals and build from there. I'm sure you're an accomplished wrench, and this seems silly- but this is where the problems lie, 9 times out of 10. I speak from experience.

Don't be big-headed about it, don't take this as offense. Be honest with yourself and don't assume "well of COURSE I did "x" right, I've done it a lot of times before". *Check and verify*.

I am in a similar boat. I have a stock 350 in a commonly-swapped frame (S10) using GM ECM made for the purpose.. and it's running like crap. So I have backed off to ground zero and am checking everything anew.