When I used to get cars in with problems like this, the first thing I did was to look at what was recently done. In this instance, because of my own ignorance, I would disconnect all the aftermarket stuff and go back to stock or close to it and of course, would be using my Tech-2 and not guessing about the BCM.
Also saw a yellow wire in that harness that looked damaged and may have arced.
any chance you put the battery cables on backwards? I knew a guy that did that to an explorer once.. basically gave up after a few days and sent it to the junk yard. it killed everything.
other than that. as said above, at this point I'd remove every single thing you've installed battery and wiring related and start from there. because as is from looking at the pics, if this rolled in most shops I know of, no one would want that job and they are just going to bill diagnostic hours and probably not do anything besides the basics.
back to doing it yourself and then at that point you're going to have to just get access, most likely paid, to a proper wiring diagrams for your truck and trace everything out. if you have all the main power distribution at where it's supposed to be. then it's time to replace modules.
good luck. electrical stuff has kinda alway been my thing, cause I'm not flat rate lol. but this one scares me.