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gremlins galore, have you tried locating and cleaning all the grounds? I've had bad grounding cause all kinds of wierd crap on other cars.
I removed the grounds on the block above oil filter, and the ones on the transmission and the braided strap to frame and the small black one to frame. I also cleaned and checked socket tension on the ECM sockets. I cleaned the block and frame with emery cloth and scotchbrite.
I know what you mean and I may have missed something. I just don't know what it might be. I'm just running out of ideas. If I listed what all I have done you would know why this thing is driving me nuts.
Two weeks ago it wouldn't run more than 20 minutes. I do have it running, but with codes. I just thought I might send one of my ECM out and get it checked out if it doesn't cost a bundle.