The trunk release, power locks, key fob, radio, interior lights, power mirrors, and the horn (horn only works when car is running) all don't work but my power windows still work great. What could be the problem? I checked my fuses and they seem fine.
Given that your fuses are fine, the logical explanation would be a break in the wiring that is common to all the affected components.
The fact that the power windows indicate that they are on a different electrical circuit.
The obvious thing to check is the area around the stereo since that is where the wiring was disturbed the most.