looks like most people have gotten most of your questions answered as far as where to get parts and info on the web.
My 2 cents, buy some doors on CL or here that are manual. Keep the electric ones to cut into half ones. Bill is right on telling you to keep the frame on the doors, I just got done making my own door covers like Bill's. Huge difference when driving in the cold even with the top off.
Rear window problem could be related to a rusted track. My truck had the same problem, still sort of does. I took it apart cleaned as much as I could and greased/oiled all I could. It works pretty well but still looking for a new tailgate.
I also recommend plywood for the sides, my old runner had rear steel panels and besides the sound they got hotter than........well you know when they were in the sun with the top off or on.
Before buying parts from a yard check here and CL first. I got a ton of parts on both sites. I will be selling some stuff during rally, another great source, as will a bunch of other folks.
If you need some help or ???? just let me know.