After some snooping around on Alldata using the freebie DIY section for the 2003 Bonneville I believe the little hub splice connector is for the taillights. The color code matches anyway.

Also, from the freebie at AllData - this shows the connections to the various door modules.
Connections - Door Modules
That should give you an idea what each does.

Have you checked all of the fuses in the rear fuse box? In particular fuse 25 (Pass MDL) and fuse 18 (RRDR MDL)? Having voltage at the orange wires (12v) would indicate that they are good, but it would be a good idea to double check.

bailey, off topic question for you, did you cut your rear carpet section in half?

Yes, I did cut the carpet

I need the car to be functional as we only have the 2 cars and we need both to get back and forth to work. I only have my days off to work on it and it'* a lot of work to rip out the complete console and both seats. I'm not sure how I'm going to protect the new seam yet.

Besides, carpet is relatively cheap.

:? ehhh, not really. that rear piece is nearly $200 at the dealer

Bailey, don't know if you still have an issue here as it'* close to 2 weeks. The same symptoms you've shared are ones I experienced a while back (maybe 2 years ago). What was happening (just as you mentioned) is all the water on the driver'* side eventually messed up the electrical system and functionality started to disappear just as you stated (remote control stopped working, interior door locks, etc.). It got worst over time. I took mine into the shop/dealer and they fixed it for around $200 (thought that was rather reasonable). I believe there was basically one wire around the kick plate area they respliced (believe it got corroded from all that water).

I'm pretty sure I can find what wire they messed with. It could be the same thing you've got, but I'm not too electrically inclined (which is why that went into the shop).

Fixitall, Still have the same issues. I haven't been working on it as I've been working for almost the last week straight. I just got my radio display lights fixed ($25) and reinstalled it tonight. The replacement heated seat switch just came in from Morad Parts on ebay and I'll try to install that this weekend. I also plan on ripping apart the drivers door to check it out.

Any info you could offer would be great. Thanks.

If I don't soon free up more time to work on this soon, I may have to take it in to the dealer

When the electrical guy at the dealer fixed my problem, he didn't remove the door panel (though that may or not be where water is entering your vehicle...could be several places). Water on my vehicle was/is entering via the kick panel area that you provided a pic of. It was behind all that stuff (needed to pry it away so I could see the metal surface beneath). It could be the same wire that electician cleaned & respliced since your symptoms ring a bell with what happened with mine. I'll try to look for it this weekend and see if I can get software installed to snap a pic and upload it (which would be ideal) so you can see what I'm talking about.

I've located the water leak today. The drivers door water shield seal leaking at the front drain location. Hopefully on Wed. I'll get new sealing caulk and get that all fixed up.
All the connections on the driver'* door module looked good.

Power functions still all wonky.

Installed new heated seat switch today - backlight bulbs burnt out on one.

This may be no help but we had a similar problem with my sons PT cruiser. We had the battery disconnected doing some work and the next day no action on the passengers side. Metered everything(no manual of course) and eventually ordered a new dash switch. Before it arrived the young lad left the lights on and drained the battery flat. When he boosted it to get it going all was working. We blame it on stray electronic gremlins known to inhabit this part of the country.

Richard