Batteries are where? Trunk?
Need some info.
What is the voltage on input stud on distribution box in trunk to ground to it's right?
What is the voltage on input stud on distribution box under hood to ground to it's right?

Get under the dash at the OBD port and tell me what voltage you read between pin 4 or 5 - one of the center pins on the top - the top being the wider side - and pin 16 - bottom right - bottom being the narrower side.

Nearly everything in car - lights, etc - need the processor in the BCM to be running.

Also, is there any chance that there was a polarity oops when reconnecting the battery?