Mark,
After reading thru this several times, I am trying to figure out what happened to the original ECM. The Electronic Control Module has Rom, Ram and an EEprom. It is designed to allow for a chassis batteries replacement. It does not have a CMOS memory battery internally to sustain information. When 12 volt power is restored, it boots up the ROM to restore all the internal programming. Cat has the ability to access the EEprom to change its parameters that govern engine performance. The only thing I can guess is that perhaps reverse polarity from the chassis battery may have damaged the ECM. But even that is only a guess because you would think Caterpillar has enough moxie to cover a potential mistake like that! Wish I could help further, I still think you need a Caterpillar technician with Cat computor software to analyze your present condition. Fred