While searching for a solution to my problem (flashing interior lights linked to faulty rear door latch I think), I read many posts about flooded footwells due to the battery drain plug blocked. I decided to check mine and thought I would post the steps - it may help someone....

First step since you are removing the battery is to check you have your radio 4 digit code. Luckily my code was in the BOSE radio manual (photo 1). The code was on page 24 (photo 2).

Disconnect the battery drain/overflow tube (photo 3) then disconnect your battery (negative first of course...)

With the battery out now remove the Battery tray by removing the 2 nuts and 2 bolts that secure it in place, then to remove the actual tray you need to 'encourage' the tray corner past one of the locating bolts (photo 4)

Now you can see the drain plug, pop it out with your finger and clean it (photo 5)

Photo 6 shows the drain removed.

Photo 7 is the actual drain plug itself.

 

My 98 A6 had water running in above the brake pedal. I cleaned out all the drains. Turns out the seal around the the black box in front of the steering wheel, sorry don't know correct name. Wires run from it into the car. It only has a like a 1/4 inch lip around it and the foam was rotten. There are a few screws, one in the back too. I did not unhook the wires, I lifted it up a little, removed old foam, and had other person apply silicon seal around the metal lip. You will need popsicle stick to get it applied all around. Set it back in place. Never had any more water issues.