So, after hearing about how the 42 pin connector can chaff by rubbing against the valve cover, I decided to investigate.
The red wire is pin #24--12V to the IPR, Fuel pump relay, the PCM relay and two pins on the 4R100 connector.
Can't imagine that wasn't causing problems somewhere, though I must admit, I have never blown a fuse.
Just cut it where the chaff was, stripped back a 1/4 inch in each direction and put in a butt connector. Then, wrapped everything up with a few layers of that good 3M electrical tape.
Truck restarted without a problem, I still haven't gone anywhere with it, so I don't know if I really solved any issues. I'll run codes later and see if anything changed anywhere.
I would recommend if you've got oddball problems to disconnect this harness and check it out. Just open the air filter housing, loosen it at the connection it makes at the engine, then, a 10mm bolt on the 42 pin connector and flip it over. You may even see a spot on the valve cover where it is rubbed raw (like mine).
Buy good electrical tape and tape up a few layers around the wiring bundle before you put everything back. They just didn't put wire loom up high enough on this harness . . .