I have 125K on my 02 SR5 and I have not had any issues except a CEL for a multiple cylinder misfire. Oh no, I had to go to the dealer and spend $18 on spark plugs LOL!
As far as the saggy butt, that is common on all 4Runners from the first 3 generations. I personally don't have that problem (lucky I guess) and I tow all kinds of stuff just because. The butt barely sagged when I was pulling a 93 Civic hatchback on a heavy ass Uhaul double axle trailer.
As far as the front window, it could be the window regulator itself.
The electrical gremlins puzzle me too. Someone said something about it sounding like it might be a flood car. I hope that's not the case but that is kinda what it sounds like it is. I have never heard of a 3rd Gen with this many electrical gremlins.
The sunroof, have the tracks been greased? My CRX had that problem and it was there was a bunch of grit in the tracks so I just had to clean them out and regrease them with white lithium grease. It's been fine ever since.