this sounds like there is still some battery damage. Specifically I believe that
1) Some of the traces between the second CPU (not the ModyPoly) and the DCO ICs are broken
2) Sometimes the internal connectors are doggy, try wiggling them and see if it improves
Thanks, I’ll look into the area you’re talking about some more. I spent some time with the schematic as well and traced all the components along the CV trail that I might try replacing as well.
It’s a shame the shop manual is so poorly scanned.