I realize this is an old post, but I thought I'd throw my 2 cents in. I've had the same problem with my '98 since I bought it. When I first noticed it, it was just wet under my front passenger floor mat. Then it seemed as though the location of the leak changed because the water started puddling up on top of my rubber mat. I popped the hood and realized 2 screws were missing from the plastic wiper cowl so I replaced the screws and siliconed them. This seemed to work for several months and I had no leak...until....
it snowed about 8 inches here the other day (not common here in MS) and I guess as it melted it ran into the truck more than ever!!! I was parked on an up slope and lots of water ran all the way under the back seat. I had to soak the puddle up with a towel and still trying to let it air out. I popped the hood again and realized that there were 2 more screws missing that I didnt see before. I've replaced and siliconed again and I'll know if it solved the problem the next time it rains..or snows.
These screws were obviously left out by the people that replaced the windshield. Anyone with this leak should check to make sure their screws aren't missing.