I had a similar problem. My carpet was getting soaked on the passenger side floor board only. No sign of wetness at all on the sides or the front running down. What I found was really sneaky and I'll try to describe it as best I can...
I removed the kick panel and ran a slow stream of water down the windshield, letting it run down the cowl to see if the water made it's way to the weep hole. What I saw was water "bleeding" through an area of fiberglass between the large oval vent opening and the square opening where the weep hole is located (also a great space for speakers...I installed Infinity speakers there, 4x6 square plate footprint) . It made a small but thick stream of water that snaked down the side and puddled on the floor never even getting the side of the carpet wet. I "patched" it with some silicone sealer and it seems to work (for now).
Hope this helps a bit.