I have a 2000 Bonnie that sat for several months while I saved up the $ to replace the transmission. On the way to have the transmission repaired I noticed that the front passenger side and both rear windows and power door locks would not work from the drivers door control or the controls on those doors. This was approx a month ago.
From reading other topics on here it seemed like this issue was most likely caused by the drivers door control module and I was going to look into it the first free weekend I had.
However, on Monday I got into the car to go to work and noticed the key fob did not unlock my drivers door, it had worked fine before this. Upon further investigation I noticed the key fob also no longer opened the trunk and the power locks for the driver door no longer worked, again they had worked previous to this. However, the drivers power window will still go up/down. Then this morning I noticed that the read defogger is no longer working.
What I am looking for is any ideas on where to start with troubleshooting and ultimately repairing this issue. I seems to me that the drivers side wiring relay (located under driver's seat?) is the best place to start, but I'm open to suggestions.

I seem to be narrowing down towards a possible cause here. I took the driver's seat out and lifted the carpeting, there was quite a bit of water under there. I got that dried out. I found two peach wires w/ white stripes in the wiring under the drivers seat. they met at a white connector labeled "T3 PED". The connection was corroded and fell apart while I was examining it. I cannot seem to locate this connection in the wiring diagrams. Can anyone tell me what these wires go to and if their no longer being connected could be causing my problems.
Also, any issues with me just splicing them together or should I use another one of these connectors (if so where can I find one)?

The closest that I can find for that wire coloring in the doors schematics is tan and white. If that is it, it is for the simple bus interface, which handles all of the communications from the driver's door module to the other modules. That could be the cause of at least some of your problems. While you having things apart, check all of the wiring and grounds that you can.

Cleaning up the wiring, solder things back together and seal each connection with heat shrinkable tubing. Then tape it all together with some good automotive or electrical tape.

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*Gone, but not forgotten* - Black 2000 SSEi, HIR Headlights, Angel Eyes fogs, 3rd brake light overlay, hi-flo cat, 180 degree thermostat, HS 1.9 rockers, LSx yellow springs, Intense FWI, PCM, shift kit, push rods, and 3.4 Pulley. ZZP Power Log.

I guess tan & white works. I made that connection and now I can control all of the functions on the passenger door. Entry lights, key fob, trunk popper, gas door lock, rear defog and all rear door functions still do not work but I am getting closer. I will have to do a closer inspection of the wiring as that was the only obviously corroded area. I will keep posting my progress, just in case other people have this same issue.

You may want to start checking around the rear integration module. Many of those functions are controlled by that.

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*Gone, but not forgotten* - Black 2000 SSEi, HIR Headlights, Angel Eyes fogs, 3rd brake light overlay, hi-flo cat, 180 degree thermostat, HS 1.9 rockers, LSx yellow springs, Intense FWI, PCM, shift kit, push rods, and 3.4 Pulley. ZZP Power Log.

Where is the rear integration module located?

Behind rear seat back cushion (upper, left)

Right rear of the passenger compartment, behind the rear seat back

These are the things that it controls.

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*Gone, but not forgotten* - Black 2000 SSEi, HIR Headlights, Angel Eyes fogs, 3rd brake light overlay, hi-flo cat, 180 degree thermostat, HS 1.9 rockers, LSx yellow springs, Intense FWI, PCM, shift kit, push rods, and 3.4 Pulley. ZZP Power Log.

So I have checked all of the wiring to the RIM three times and have found no issues. I am thinking of trying replacing the RIM, anyone have any other ideas? Or know a good place to get one?

I have several for sale, PM me.

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Andrew - owner/operator of Bonnevilles Unlimited

2004 Bonneville GXP | 60k | White Gold Tricoat | custom built supercharged 3800 hot rod | garage queen
1997 Corvette | 55k | Silver Metallic | Z06 wheels | Date-night Hauler/Parts runner
2014 Town & Country Limited | Cashmere Pearl | 95k | Family Hauler
2002 Ram 1500 Quad Cab Sport | Black| 260k | Official Bonneville Hauler