Crew Cab Sonoma LQ4/4L80E Swap

Hey everyone, I'm new to this forum, but not forums. I've had my 2002 Sonoma for just over two years now, and built it into the prerunner it is over 14 months from the time I started cutting into it to its first drive. It's a different route than most go with these trucks, and it has been working awesome for me. Here's some specs and pictures before asking my questions.

Chopped frame in front of the firewall and grafted 1993 Ford Explorer frame with TTB and steering box. Cut and extended the beams and axles 4.5", pulling 16.5" of travel bumped and strapped. No driveshaft yet as I've been anticipating a motor and trans swap.
I cut the rear frame immediately behind the cab and rebuilt it with 1/4" wall 2x4 rect tube and 1.75"x.120 DOM tube. Schreiner 31 spline full floater 9" axle, 4 link suspension, 2.5" kings all around with king bumps, 35" tires, 5.29 gearing, caged front to rear. I built every component on the truck myself in my parent's driveway, including all the paneling, center console, etc. Had to modify the rear fiberglass to fit since nobody makes shortbed glass...














Last weekend I picked up a 2000 2500 with the LQ4 and 4L80E to swap in. The 4.3L isn't the worst, but it has a solid misfire, leaks a heavy amount, and the 4L60E... sucks something fierce.




I am very confident with fabrication and mechanic work. I have no hesitations with getting the drivetrain in place and plumbed. My hesitation lies with the wiring. I do not really have a great understanding of how everything in the truck talks to each other. I can figure out basic circuits and troubleshoot, but I am getting totally lost with the wiring. Note, I haven't started any wiring, just trying to plan it out. I've done a ton of searching through various forums, but haven't found an explanation that helps.

Since I have the entire donor vehicle I will be able to take the entire wiring harness and ecu and use those (I know I'll have to have it tuned to adjust shift points and axle ration/tire size).

When I compare the pinout for the 6.0L to the pinout for the 4.3L they are incredibly similar, with very few minor differences. I read that everyone who does their own wiring changes the pin locations, but why would I need to do this if I'm using the 6.0L harness and computer? Are the pins to the fuse block the ones being changed, or the pins to the computer? Do I just need to connect the ECU to the stock BCM?

Please help break it down for me. I'm not looking for a step by step procedure, but a more broad overview would be helpful (IE: Use the stock LQ4 computer, but needs to change to talk to ). I'm trying to save some cash from the Current Performance harness, but it's not out of the question.

Here's the pinout readings I'm using
file:///C:/Users/bodja/Downloads/PCM%20Conectors%201.pdf

Thanks in advance for your help!