Long ass thread, not going to read 25 pages. So sorry if I'm repeating anything
I'm wondering if it's cycling back and forth between lean and rich, and misfiring on lean. And you might have an injector that's underperforming to the point of misfire. Either rich or lean. Not sure what the GM spec on it is on the new rigs but I seem to recall reading somewhere a while ago that the tolerance for flow on older rigs that +/- 15%. I'm unable to locate that at current to take that with a grain of salt.
Sooo, my thought is this: See if you can find a good scanner. Figure out which cylinder is misfiring, if it's even tripping the misfire monitor. Cross reference that with the commanded fuel flow and/or oxygen sensor voltages.
If possible, see if you can tune or otherwise command the rig to run a bit rich to see if that alleviates the issue.
You might also try investigating your spark plug gaps. Narrow them down a few thousandths. See if there's some weird intermittent weak spark