The reason Im not really convinced its a communication problem is the modules that threw the Uxxxx loss of comms codes arent really related to the TCM. That and they are history codes, so the diagnostics passed during the last ignition cycle. (maybe they were set when you disconnected the batteries when you put the trans back in??) Even if there was a communication problem with the TCM I cant really see how it would cause this issue?? The NSBU wiring is all discrete; nothing goes through the data bus. Only problem really a loss of comms would result in is inability to read codes from the TCM, a loss of PRND321 display, a loss of the trans temp gauge, and the doors would not automatically lock when you put the truck in drive.