Honestly, I think I'm pretty good at this and I'm not sure how I'd go about this one. The overarching doubt is whether we have a single or multiple points of failure. If it's single, logic says it's the Body ECU. But that does not address the window issues, which should be immune from the Body ECU. Further, you have swapped the master switch and, to my honest surprise, no fix on TWO problems, and again, that's the only place those two overlap.
These machines are relatively reliable as to electric, and when I see multiple failures, I tend to think common cause where possible, and that is usually right. In your case, I'm starting to think multiple, but related, points of fail.
So, what do we know about the history of this vehicle? Did you run a Carfax? Any chance this thing has seen a flood or immersion? Is the carpet water damaged? Or new? Water in the headlights? Any other clues?
Anyway, I am not going to think single point of fail, because I don't believe there is one. So let's decide to track down one issue that is, or should be, relatively easy to chase--that rear window and see what that tells us.
Wait for my next post....
[MENTION=102597]IBallEngineer[/MENTION] Old man, (but younger than me), how do you figure Body ECU could cause these window issues?