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What sensor could the previous owner have possibly disabled for the alarm that would cause all the issues I'm having:
1) Automatic Lights won't turn off when exiting door
2) Interior lights won't come on (only passenger door)
3) Alarm doesn't work
4) Door Locks won't work (thinks door is always closed I guess)
PO said something about the alarm and a door sensor but I can't figure out which one it might be.
Numbers one and two could be the result of a bad door sensor. It could be partially responsible for number 3. All of these symptoms may not be related, they could all be broken independently.
I've only been in this game for a few weeks, my car didn't come with an owners manual and I don't have a shop manual yet either. A friend had a similar experience, he bought a 95 Corvette for about half of book because it wouldn't start. It turned out that the drivers side door sensor went bad which kept the theft system engaged all the time which eventually burned the wiring and caused the no start.
Just to update, everything was related to the harness going to the door. The ground cable is completely stripped and the red wire was chaffed in two places from the window going up and down.