I'm not sure if it was smart or not, but I checked out each fuse from the fuse box to make sure they were all okay (after having to replace one that wasn't).
Well, now there's a few problems.
Everything was working perfectly fine beforehand, but now the power windows don't work, the lights don't come on when a door is opened, the ESP light is on, and the trunk release doesn't work (both the manual-electronic one in the door, and the remote). So far, those are the only problems i've encountered.

Any ideas on what could've happened, or how i could fix what I did? The fuses are still okay, but maybe I reset something by pulling one of the fuses out?
Any help would be appreciated.

 

i would take the one you replaced off also sometimes you need to disconnect the battery before replaceing , disconnect one you replaced and if that dont work try disconnecting the battery for about 5 mins and reconnect it and see what happens

 

Okay, just got back from a short drive. The ESP light is off, but the power windows, and the sunroof still don't work. Once I parked the car, I also tried the inside trunk release, but to no avail. I also found out that the motion alarm sensors in the door can't be switched on (the ones right above the trunk release). The remote still does not unlock the trunk either.

 

one time i had the same problem i was driveing and all of a sudden i could not close my sunroof i was worried because it started raineing what i did was i disconnected the battery it reprograms everything but for like 5 mins then i went inside and tryed closeing it and worked i kinda called it a glitch a eletrical glitch try doing that

 

the only thing is sometimes you can un program your key fob by takeing out the fuse and then your key fob wont work and its a bitch to reprogram because you need to keys to do it , but their is not reason for your windows to not work and sunroof try disconnecting it for 5 mins and try again you dont need to drive it to do it lol

 

also did you replace all your fuses with right amp? try finding a diagram just to make sure if it does not say on the fusebox

 

you probably put some fuses in the wrong place or they're not in securely, or now one of them is blown. check the fuses for the parts that are not working.

 

Aha. Turns out, fuse 24 (the Central Comfort Electronics fuse), was missing. Now, I didn't misplace any of the fuses, as I carefully pulled them out 1 at a time, and replaced them each before pulling out the next one, so how this system was working without the fuse before, is perplexing...
Well, i added the fuse, and viola! Everything works good as new. Seriously though, I do appreciate all the suggestions and help you guys have offered. This is my first Audi, so you can bet i'll be around these boards with more questions.
Thanks all!