Thanks for the input guys.
I spent all day on it. Like 9 hours. I took a ton of pics, but I don't have time to upload them and really do a write-up on it tonight. I'll start another thread for the write-up, since there's not really a great one that I've found.
I'm glad I did all this though, because there was a bunch of mold growing the headliner from all the water in it over the years. My sister owned this thing for like 12 years and apparently the sunroof has been leaking for like 11 of them. Man that thing was gross.
As I said in my first post, the sunroof doesn't operate, so I couldn't get to the drains in the sunroof "tray" itself. The tubes were pretty gunked up, so I ran weedeater line down the tubes and then sprayed the hose through them to clean them out. Side note - the drains run into the rocker panels? WTF Toyota? Can't wait to get road salt in there...
Then the sunroof assembly came out, and I cleaned it up as best I could. The mechanism is a giant clump of rust, which explains why it doesn't work, haha.
The headliner itself was a mess, so I bleached the top side (facing the roof skin) to kill the mold and left it in the sun for a few hours. Then I rented a rug doctor and cleaned the upholstered side of it as best I could. It's not brand new, but it looks (and smells) a hell of a lot better. The seats and as much of the carpet as I could get to without pulling seats got cleaned too. The recovery tank in the rug doctor looked like it was full of Guiness.
Putting it all back together, especially the sunroof, is a two man job. I did it by myself but I feel like I got hit by a truck after wrestling that thing all afternoon. I used some clear silicone around the sunroof, but I think I probably need to go back and hit a couple spots.
tl;dr: don't buy a car with a sunroof.
__________________
2001 SR5 - Like OEM, only worse (gears, e-locker, armor)