I've always heard it was bad to spin a transmission in neutral at high speeds. When you shut one of the engines off, do you leave the transmission in neutral?
I still see a problem with the 2 engines being out of sync. They're not independent of one another because they are part of the same chassis. No matter what happens, one engine is dragging or pulling the other, because they are physically attached to one another. I don't know fit that is what caused your transmission issue, but time will tell. I would think it'd be odd to the PCM because the transmission is being drug through each shift. When a typical car shifts, acceleration stops during the shift...not here though.
