It turns out that in the process of me pulling all the fuses and relays, I just so happened to put the "instrument cluster" fuse in the wrong slot. There was no effin fuse in there! That what caused all my gauges, radio, windows, etc. not to work. I replaced the fuse and I was back to square one.
After pouring over the wiring schematics for the truck, I narrowed it down to the brake pedal switch (as was suggested by many). At first I thought that there were two switches. The plunger actually turns out to be tied to the cruise control. After I removed the actual brake pedal switch, I disassembled it. On set of the contacts was messed up. There is a little piece of plastic that holds the arm away from the contact that was broken.
I shimmed a piece of paper (lottery ticket) in between the contact and the arm and reassembled the piece. I installed it and now my brakes don't stay on. YAAAAYYYY!
So tomorrow morning, I'm heading up to the Ford place to speak my mind to them. It's pretty sad that their "trained" techs couldn't figure out that it was missing a fuse to make everything work. Instead they just wrote it off as a bad junction box worth $400 in parts and labor in hopes of "fixing all my problems".
Believe me, I don't think I will ever go back to this dealership for any work. In the time that I have spent diagnosing the problem and chasing stuff based on their misinformation, they should be paying me $400.
Sorry for the rant....It just frustrates me. At least now I know the problem and can now fix it.