WTF Electrical problem

I drive a 2000 Eclipse, 2.4L 4 cylinder, 5 speed manual.
6 months ago i removed my battery to take my subs out for about 20 minutes. When I hooked it back up, I noticed there is no power to my radio, power locks dont work, sun roof doesnt work, driver side running lights (front and back) dont work, running tailight doesnt work (brake light does), fog light fails on driver side only, and my headlights require the car to be running now to be on.
I've taken it to 2 shops and $900 later, no results. Ive checked all the fuses in the compartment, back of the stereo, by the pedals, in the engine compartment. I even swapped the relay switches to test them and nothing changed. Wires in and under the dash look fine -no pinched wires. No bad wires in the engine compartment either. My only thought is bad ground but that doesnt make sense since I didnt touch any of them.
Any ideas would rock! 6 months, no radio really bites and Ive picked up a wiring diagram finally too.
Thanks again

Well, my only new idea is a body control module of some sort may have gotten fried. Looks like i have 1 that controls most of my interior features and the window relay is on its own switch which is why they work. Any one know what this looks like and where it is? Think i may know but any solid thoughts would help a ton.
Thanks again

Not sure where it would be but this sounds like a good place to start. When you were taking them out you didn't happen to have any power hit the frame anywhere did it? If so this would have fried several components as I have seen it done before on a vehicle...