We got a bunch done on Saturday night. Removed everything related to the auto from the harness. Installed new axles, put the exhaust back together, programmed the ECU to manual, verified cruise and revese lights worked. Waiting for the power steering line, as the auto goes over the transmission while the manual goes under. That should arrive Wednesday.
So, Wednesday night we should be done. Just have to do some coolant stuff, the power steering line, and change out the valve cover. Probably a couple more small wiring things, then it’s done.
Edit: Here’s a sort of before picture of the wire harness mess: