Why don't you take a water hose to the trouble areas you think may be causing the leak and see if water comes through.(ie. the windshield cowl, the side windows and the door seam)
I have had my car fixed since may and it has rained like crazy the past week and my floors are still dry. The problem that the dealer found is that the weld seams along the firewall were pretty *****ty and it allowed a ton of water to leak into my car. They sealed all the weld seams and let it sit for 24 hours to cure and ever since then, I have had no water. Just tell the dealership to do the same beacuse that seems to be the problem in most cases.