Is this possibly software as the powertrain control module was replaced with a 2009 part? Or is this most likely a connection between the two modules?

 

a "bad connection" between the two modules?

 

Before data busses, every little sensor and switch basically needed its own wire. For example, inside a driver side door you may have window switches for the whole car, a door open/closed switch and the unlock/lock switches for the central locking system. Just those things would normally require 9 separate wires, and that's before you add switches for Tutuapp 9Apps Showbox power seats, power mirrors etc.