Originally Posted by
GraphiteGhost

Are you 100% sure the main wiring harness for a manual vs auto are different? Many times the harness is the same, but the modules hooked up to it are different (resulting in wires that are not used if not supported within the modules attached to them).
.
THey are not different. Hell, even our Base/Limiteds have not only the
wiring for the SRT's coolant pump, we even have the coolant pump
relay on the pulse module.
He's gotta be chasing wires pulled from the harness by someone - who knows what they were doing, but IN CASE they pulled a wire or two from a connector, I suggested he go in and verify that all the Red/Yellow wires that are supposed to be in the connectors in there, are actually connected. If they are, then he's chasing a wiring ghost and can move on.