Off hand, I can really only think of two places where there are holes in the body to the outside in that area.
1) In the door jamb near the hinges, there's a connector for the door wiring (power windows/locks/mirrors/speaker). Check that and make sure it's fully seated.
2) The firewall has holes for the steering column, brake plunger, clutch, cruise cable, etc. Check to make sure all those are secure.
Otherwise, the seal around your windshield could be leaking, I suppose. Open the hood and have someone hit everything in the area with a garden hose, pull the carpet back and see where the water runs.