I have the same problem in my 02 Impala. The water seems to come up from underneath. For a few weeks before water started collecting in the rear floorboard, I could hear it slushing around when I hit the brakes quickly. Sounded like it was coming from inside the rear passenger door or under the cabin on that side. All the seals around my doors look good, and like your problem, it seems to be coming up from underneath because the sides of the floorboard around it are dry.
I'll look for the plugs when I get home, but just wanted to see if you had noticed the sound of water slushing around inside your car. Sounds like making a hole is a temporary fix. Any ideas on a permanent fix, or could it be a number of things that needs to be looked at personally?
Thanks,
Jason