I haven't forgotten about this, I've just been extremely busy.
What I'm wondering is if you lost data communication between the Driver Door Module (DDM) and the other three door modules. I need to review some diagrams to look for routing of the data line. There are also a couple of other possibilities as well.
The fact that there is water underneath your carpet is quite concerning. Most connectors are up and out of the way (unless you had an excessive amount), but it'* still possible that this could be moisture related. I'll come back to this once I've had a chance to look at diagrams and routing info. Regardless, you really need to find the source of the water because even if it isn't somehow related to this problem, it will cause you grief down the road.
Two possibilities are clogged or leaking sunroof drains. The other, and very common in the 2K+ Bonneville is leaking water deflectors behind the door panels.
Have a look at these threads...
the 2000 sunroof drain fix (20+ 800x600 pics) - Pontiac Bonneville Forum - Official home of the Pontiac Bonneville Club.
2000 - 2005 Water Leaks. Drying them up! - Pontiac Bonneville Forum - Official home of the Pontiac Bonneville Club.
I'll post back on the original issue as soon as possible. I have a suspicion you're going to want to pull the driver seat out and have a look underneath. If nothing else, make sure it'* dry under there once you find the source of the water.