I have the exact same problem with my hard top. I get water build up on the carpet right at the back edge. To me, it looks like the water is running down the inside of the back window and settling there at the bottom. I've checked the window and seals out thoroughly, and everything appears to be in good shape. If anyone could help assessing this issue, is would sure be appreciated.
As for the pressure/vacuum you have with closing your doors when the windows are up....
I really wouldn't worry about that. Mine does that too. In my opinion, that's just a sign of a good seal between the hard top and body of the Jeep. I'd be more worried if it DIDN'T do that. It would make me think that something WASN'T sealed up the way it should be.
But if it really bothers you, just barely crack one of your windows before shutting your door, and the problem will go away.
(Not recommended when parking in rainy and snowy conditions)