I'm starting to get clear headed enough to read back through this...
The 2001 didn't have a SC option; it was only available in 2002-2004. Also, the truck would have a myriad of body style changes such as a bulbous hood to indicate that it's from that time period. I'm starting to think that the previous owner did so much mucking about that maybe the O2 sensors are backwards or something. They're close enough to be in spec, but are telling the computer to trim the fuel on the wrong bank.
Dubious wiring (those red ones) I'm wary of with no documentation. I'm also curious as to why the O2 connectors are so short...
<looming>
The factory looming has 3 penetrations in the firewall : Driver side near the fender, passenger side near the fender, nearish the center for the engine. The engine harness is the main trunk line in your pictures that runs along the upper intake. There's 1 connector, gray, that breaks off nearer the start of the run and connects down to the transmission and transfer case. I can't quite tell the color of the connector in your hand.
<the Trio>
Do you have a working window wiper? I'm still not sure on this one, but there are two connectors back there, but I don't think the colors match. The other one may go to a factory security horn; black connector with only 1 wire in it.
<intake>
Pulling the upper intake isn't that hard, just really frustrating at times. Be prepared for the captive socket bolts to strip. When they do, grab a deep 12mm and beat the tar out of it to wedge it over the bolt head. You should be able to drive the bolt out with it on like that. End result:
There are also two coolant lines at the back. Save yourself some headache and cut them. I spent way too long trying to undo ONE of the hose clamps back there.
I'll keep digging.