You aren't going to want to hear this, but you probably need to take the right hinge off and find the wire that got pinched under a bolt head or hinge. It's either that, or something is plugged in wrong or grounding out down in the door. I'd have to open up mine and look at it while contemplating your symptoms to narrow it down any further.

I just did mine last weekend. I don't replace the wires, I just cut out the bad (brittle) section in the wire and solder it together, and pull up the harness a few inches to get fresh wire through the hinge. I spliced in 1 ft extensions to the wires down in the door the first time I did it years ago, so that I could fix it this way several times (I'm really cheap; Scotch, ya-know).

You already know what tools you need (ratchet, deep socket, Torx bit) so I presume that you are wrestling with the door itself.

I disconnected the shocks that support the door, and supported the door with a couple of short 1" x 2" sticks threaded through the door handle. One end of the sticks rested on metal just below the window, the other end stuck out and rested on a step on my stepladder. I then laid a 1" x 4" on the roof of the car and when I removed a hinge, I slipped it rearward so that it supported top edge of the rear door. When the hinge was bolted back to the door and was ready to screw back down to the roof, I slipped the 1 x 4 out from under it so that the hinge would settle back down in its spot.

It was cold, which made the wire and the caulking stiff and hard to work with, but otherwise, there was no problem.

Any car that costs you less than $10k (and some that cost more) will require periodic repairs. Even if you break something once in a while, it is a cheap education and you will be money ahead in the long run. You can do it. Just remember to work smart, not hard. ;)