To me, your questions are much too broad for anyone to answer on the forum. Someone would have to be there with you to see exactly what you have and what you don't have. I, at least, am a hobbyist not a pro.
Suggest you run a Google search for a factory service manual, or maybe someone knows of a website. Being an experienced mechanic, you can make good use of a complete set of wiring diagrams.
You're stuck on the missing parts unless you have detailed bill of sale. You need legal help on that score. The service manual will have the parts list so that you can match them up with what he gives you. Otherwise you won't know if he is still ripping you off. As you know, there are a zillion little things as well as a few big things.
"Blessed is one who gives without remembering and receives without forgetting." Rabbi Eleazar, 1250 AD
93 YJ project. 4.0L, stick
MJ-7 re-body, Banks header, 2.5 " pipe, low resistence cat, Flowmaster. K&N filter thru a snorkel.