Seeing as I didn't do anything except let it run for a few hundred miles and it went from sputtering to purring like a kitten, I'm confident of my root cause analysis.I am sorry, your hypothesis does not sound plausible to me. There is something more going on there that has nothing to do with ECU settings on basically clearing of common "adaptives". Your last comment makes more sense, or you pulled a wire out of a sensor/coil/ect.. by moving stuff around.
I didn't touch the coils, just changed the battery. The OP did a bunch of stuff.