I had this exact same problem recently. The water was coming in at the very bottom of the door and running over the interior plastic door sill. I did some searches on this site to see if anybody else had had this problem and eventually concluded that I had a problem with the polyshield.
It appears that the problem with our doors is that the glue that holds the polyshield (a thin foam-like sheet that covers the entire interior of the door) has a tendancy to come un-glued. I took the door panel off to to investigate and hopefully fix the problem and found that my polyshield was unglued in a number of places particlarly along the bottom of the door and that it was also soaked in one place in particular where it seemed the water was coming from. I attempted to fix the problem by re-glueing the polyshield where there were gaps with some RV sealer/adhesive. I didn't think I had done a very good job and suspected that I would have to replace the whole polysheild but we have had 2-3 hard rains since then and I have had no water on the floor of my car.
One word of advice, if attempting to remove the door panel definitely go to the "Door Speaker Install" thread in the Capital CEG branch directory for some essential tips.
