Ben, nice work. My '79 was similar; a good body shell but lots of other issues that kept it from driving. Mine seems to be more hydraulic systems problems, but plenty of wiring issues as well. I found a lot of places where the insulation had become hard and broken off, leaving exposed wires. So I can relate to any frustration you must have experienced, but also the feeling of finally getting things to work.
Regarding the headlights not coming up. One possibility is the two diodes that are connected to the motor on each light. It is very common for these to fail. Though it's a bit odd that all of would them fail preventing all function of the motors; usually one light will go up but not down, or both will do opposite functions, or other odd behavior. So if yours are not responding at all then it might not be the diodes. But keep this in mind, who knows. Sometimes after one fails another is overloaded and also fails, etc. I'll include a link about it below. Also check the wires around the motors. They are subjected to movement every time the lights go up or down, plus exposed to the elements, road grim, etc. I had a couple wires there that were either broken completely, the insulation had come off allowing the wire to contact a ground, the connection was displaced, etc. And like all wiring issues, check the grounds and connections.
I think it was wise to retain the unused wire harnesses for the AC and heat. The systems are complex and cutting things out may have lead to further problems. Plus like you said, who knows if you might need to reinstall something later.
Diodes:
http://www.visualimpressions.ca/fiat/diodes.htm
