Just a thought, May be redundant with what you have already gone through.
I ran into an issue similar to what you are talking about. After pulling hair out for days the end result was, for lack of a better word, a floating ground. Check battery voltage, then check battery positive to engine ground (anywhere on the block/head) the voltage should be the same if not it could be a grounding problem. Over time the “natural” ground happening through Engine / Transmission mounts will oxidize and break down. You end up with the equivalent of “Bucking Phase” in a dual source AC power system. Source 1 being the battery and source 2 being the Gen.
The easy fix was to run a ground strap to a bolt on the transmission case.
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