So I've identified the four unplugged connectors. Apparently all these cars had the same harness whether they were MT or AT and Federal or CA emissions. All the unplugged connectors have something to do AT and CA emissions so they are rightfully disconnected in this car.
I can't seem to find anything loose, broken, or disconnected that's vital. I'm confused by one particular relay, however, that doesn't show up in any of the parts lists. Does anyone recognize this:
The blue and yellow wires travel up along the firewall and into the cabin on the passenger's side:
Because of this I assumed it has something to do with the optional A/C on the car. However, the A/C relay is already accounted for, although the relay has "Window Relay" stamped into its side.
Looks like an alternator and/or external regulator problem is still the top hypothesis.