Unable to communicate with engine or transmission over OBD?

[Sphengali]

I drove 10 hour roundtrip through Washington in the pissing down rain, passengers window switch got wet and fried... then the transmission went 'clunk' and went into fail-safe mode.

After getting back home, next day I put it in reverse, and clunk - engine even turned off! I knew my battery was getting weak, so I replaced it, and reverse worked again for a day, although still in fail-safe mode. I also replaced the passenger window switch, and it too is working ok now.

I took it in to an independant shop, they said the OBD is NOT communicating with the engine or transmission, so they can't diagnose at the moment.

Any ideas what module/sensor/fuse would be at fault? The OBD can communicate with all the other modules just fine.