1 and 40 on each connector are the pcm grounds, obviously...so go ahead and get that wired up and out of the way. 2 and 20 on red are constant 12v and 19 on red is the ignition key on signal...those are the BIGGEST things you need to make sure of from the very beginning.
when i went in and did my harness, i pulled it ALL apart. got every sensor plug seperate...not a horrible idea, just REALLY time consuming. yes, i removed all the excess stuff "correctly" but i have 25 hrs into my harness and im far from happy with it. Don't really have a suggestion on what is best to thin out the harness short of spending the 300$ to get someone else to do it and make it look good if you dont feel like putting THAT much time into it. its not hard, just time consuming...
and it looks like most of the stuff in what you posted up was just where gm changed wire colors thoughout the years. I know all my PCM grounds were just straight black, but it was also an 02 harness to begin with.
check this link too
http://www.lt1swap.com/2001_ls1_schematic.htm
i used it some...along with everything else you have seen already. also, a CHILTONS manual is good to have. i bought one for that gen half ton and it has good diagrams in the back, but the pinout stuff isn't the best...but atleast you can find out what pigtail you have hanging around as a stray or what other wires need to be pulled when pulling egr, etc.
also, make sure your crank pos sensor is hooked up and wired in right...along with cam pos., sensor 1 bank 1 and 2 O2s (just to get it running a little better), IAC, and MAP. MAF is nice to have hooked up too. engine coolant temp isn't necessary, but nice to have also, since some spark tables are slightly affected by it. IMO remove all the egr, air, other emissions, etc crap you dont feel you need...because you dont. stupid crap like oil level and coolant level sensors aren't needed, and half of them dont even go to the PCM anyway. i didn't use any of the other body control modules...just removed that crap entirely and mine works fine.
The wiring on these motors is insanely simple...don't sweat it. there is really nothing to it. If i can get one running, anyone can...just make sure, like i said, the 7 important PCM wires are hooked up, grounds grounded GOOD (pcm prefers to be grounded to the head from what others have told me, and i have no issues with mine grounded to it...made my life better imo). The swap is honestly an easy one and id be more than willing to do one again. JUST DONT SWEAT IT!!! and ask tons of questions. i know i did...and mine runs like a raped ape!!
