What a job! I'm glad it's all well-connected. Foolish question, but did you also check for shorts to ground? There's a way to test the voltages on the CCD Buss, but I can't find it right now.
Another question, could one of the modules on the buss be killing it?
I'll check back in a few hours, it's waaay past my bedtime.

 

Any updates?

 

I find the whole thing very interesting, it seems like the "Bus" is just an industrial controls network like ModBus. I bet you could hook the scanner anywhere onto the bus to take readings should you think that the ODBII port is losing connection to the bus.
Steve