So I did a little research and it looks like you might be talking about the BCM?
A fried BCM seems like it could be causing my problems with lights and radio, but could it cause the charging issues too? It seems like the electronics are totally destroyed. The car is making random buzzes, clicks and flashes from every relay and light bulb on the car. I can't pinpoint any symptoms because everything is going crazy. The trunk release is even "flashing" with the lights sometimes. I'm pretty good with electronics (installed various stereos, remote starts, PATS bypass modules, even a standalone computer setup on an older car) but I really don't even know where to start here.
I don't understand how shorting one stereo channel could cause this. I'm ready to rip my hair out lol.