Think I might of found the source of the transmission limp mod from when I first bought this Jeep and drove it home.
I'll have a better look tomorrow and check the wiring schematic to see what the wires are running.
Looks like this jeep may have had the trannie out for the F37 recall and there is a wiring harness clamp on the bellhousing that the harness wasn't reattached to.
Looks like this timing belt job just keep getting bigger and bigger.