So I removed my battery on the Audi to do fix some stuff with the headlights. Now, after putting on the battery again; the windows, sunroof, central lighting will not light up when locking car or in middle position (but will work if it is in the "right" position to turn all lights off), and I'm not getting any feedback from my latch when trying to unlock the trunk door. I have a 2003 Audi A4 3.0L Avant.
Now, I know some of the common problems are with the radio, which I'm not having. I did the whole re-install of the car with the key for keyless entry, etc. I did follow the whole instruction manual on how to recover everything that was lost during the removal (5 seconds in ignition, etc) and nothing is helping the power to the windows, sunroof, back latch, and the buttons on the lower door part on the driver side for when I'm parked uphill.
Yes, the memory buttons work.
Yes, radio works.
Yes, I can push a button so the mirrors turn in towards the car.
Yes, automatic lock works.

Now, I checked all the fuses, including the ones under the steering wheel column and they are all good. I'm thinking there's a problem with the Comfort Module, but then I wouldn't be able to unlock the car keyless, radio, move seats, etc. So I'm totally lost. Is there a problem with the firewall that I've been hearing so much about? Do I just need to give it time? Do I need to get a VAC-COM (Which arrives this week) cable and fix some of the settings?

Has anyone else had these problems? Pretty frustrating.