Even though you have continuity in all wires, they are likely shorting to each other. Also, you say that when you had wires exposed, everything worked ok, but when you put back together, problem recurred......I think you were on the right track toward fixing the problem, but you probably didn't do a complete fix.

What you should do is remove inner door panel and unplug harness from window motor, and detach any brackets attached harness to door....this will give you a lot of play. Then remove the rubber boot again and pull as much of the harness out of the door as you can, leaving the end of the harness with the plug inside the door. Slide the rubber boot out of the way and inspect each wire thoroughly. Look for small cracks or gaps in wire insulation. I will almost guarantee that you will find gaps...not breaks in the copper wire, but gaps in the insulation. Remove sections with faulty insulation and replace with same guage wire. Some of the gaps may be right where the harness enters the central pillar, and you dont have much slack and working room to splice in new sections....just go slow and dont cut any corners (this is one of those pain-in-the-neck jobs that you only want to do once!!)

You must make these repairs using the very best permanent methods. What I did was to slide on heat shrink tubing before you connect replacement sections of wire. Then solder wire connections, making connections as tight and smooth as possible (this will prevent sharp points from protruding through insulation). Then put a small piece of electrical tape around the soldered joint (extra protection). Then slip heat shrink over and shrink on securely. Put together and you will likely be problem free.

Just a note..when using heat shrink tubing (available at radio shack) slide well out of the way before you solder to prevent shrinking it from the head of soldering.

That said, if you are confident that you have already fixed all wires in fool proof fashion, then you should look at are the insides of the window switches (both on the door and in the console)...they get very dirty, and contacts get carbonized, and sometimes the kill swith on the console that disables the rear door switches gets screwed up. Clean out thoroughly, scrape all terminals with a blade (both in the switch housing, and on the underside of the brass contacts), put a dab of grease on bearings, and re-assemble.

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1984 300TD Wagon, 407,800 mi (current daily driver)
1985 300DT Sedan, 330,000 mi (gone to that great autobahn in the sky)