I can almost guarantee it is the foam around the kick panel vents like NPD732 was saying. I redid the interior on one of mine recently. Put in a sunroof that does not leak, but had me thinking it was for the longest time. Right before I installed the carpeting, along with the heatshield material and carpet padding below it, I knew I needed to track it down.
The real hint came when I had stripped down the floor and hit it with some phosphoric acid, and left it parked on a slight incline toward the driver side. It rained and my sunroof was perfectly dry, but there was a trail from the puddle on the passenger side to the kick panel, and no water in the driver side.
I used a strip of 3/8-inch window sealant made by 3M. It's that black tar-like stuff that comes in a flat box, and is coiled with a strip of wax paper to keep it from sticking to itself. NAPA carries it in their paint section. It worked perfectly, and now after the heaviest rains, the floor is still dry.