So I was driving in my 88gl wagon. It has power windows and smoke started coming from under my drivers door pannel so I pulled over and took off the pannel and no more smoke. So I put it all back together and my windows wont work now. Also since then I hear a soft click from my passemger side and the battery gauge drops significantly and then a louder click right after and the battery gauge goes back up?? The clicking happens about every 10 seconds, Any ideas??

shorted wire in the door wiring.

Circuit breaker and control box under passenger seat might be smoked, but circuit breaker is cutting out.......that's the gauge dropping and coming back up as the breaker cuts out.

I'd check the heavy red wire that goes from a junction under passenger side foot carpet out ot hte doors.  There is a crimp junction with 5 red wires collared in brass.  Check that too for corrosion and re-wrap it with tape.  trace that wire up intot eh door loom to find the short.

If all doesn't return to normal after that, then replace control unit under pass seat.

That sounds right about where the sound is coming from, thank you, im pretty sure I smoked my regulator for the drivers window also, haha so im gonna unplug the regulator and see if I keep popping fuses like i have been.