Oh, and a couple of additional things... I reconnected the 3rd brake light today (has to use a TJ bracket, as the TJ hinges do not allow for the use of the YJ bracket, but I made it work), re-wired the back-up lamp (I had to relocate to the driver's side when I used the TJ tailgate hinges), and put in the heater hose valve to close the flow of coolant to the heater core. I also checked the vacuum lines of the heater/ventilation system, and they seem to be working. I have a vacuum reservoir in place, and I last drop the Jeep on Friday. Today, you could still hear the vacuum operating, which means that it is keeping the vacuum pressure, so I figured they are still good. I did notice the vent cable had come loose, but cable that operates the heater trap door (or whatever it is called) is working fine, so I guess the insulation has come loose and that is why I was getting hot air.
I did notice that behind the dash there was a positive and negative (red and black) wires that were not connected to anything. The positive has a 90* connecting boot (similar to the one on the cigarette lighter, but it's not that one), and the negative has a female plug. Any idea what those are, or what they are supposed to be connected to? I took a picture with my phone that I can post tomorrow in case you are interested...