You mentioned earlier that mechanical timing is "way down the list". Keep in mind that this is a tractor motor based on 1986 technology. If the mechanical adjustments are not to factory spec, the ECU and related sensors have a VERY limited window to bring things back. All mechanical adjustments must be done first.
X2 - remember this is essentially a mechanical/analog engine with electronics retro-fitted onto it. Get all the mechanical portions working at least close, or the electronics cant do their jobs.