I've had a passenger footwell leak in my '99 Sharan. Did as suggested to clear the drain ports, even removed the windscreen wiper mechanism. These ports were clear. After much head scratching I found where the water was getting in.
At the bottom of the windscreen there is a three section plastic trim. One long one across the bottom of the screen, and two corner quadrants through which the wiper pivots protrude. On these quad pieces there are three plastic fixing clips which are inserted into the metal bodywork, the plastic trim then snaps into these. Two of the body clips are within the engine compartment bodywork, and pose no problem. The third is located about 150mm up the windscreen side pillar where the water running off the car roof, naturally runs past the clip. The water seeps under the clip and through the hole in the pillar into the passenger compartment.
Prise the little plastic peg out the centre of the clip, then extract the clip from the bodywork. The hole allows water to run into the passenger foot well. Make sure the area is completely dry, bodge a load of high modulous silicon (glazing silicon is good) into and around the hole. Replace the clip and peg. Allow the silicon to go off, then replace the plastic quad trim. This cured my leak. Same on the driver's side.
Big Steve in Bridlington
January 2012