I replaced my driver-side door seal due to the same reason. I used a Crown seal and wasn't too happy with it; it's thicker than the OEM one and makes the door significantly harder to close, even after adjusting the latches. It also makes the door stick out from the body somewhat instead of being flush.
In my case after replacing the seal I still had water on the bottom edge of my door and new seal.
My Jeep will puddle water similarly to yours but for my TJ I'm leaning towards the windshield cowl seal. If you reach up and feel the wires behind your OBDII plug are they wet? When my floor is soaked those wires are always wet. I've even seen it in the act dripping from those wires.
I just got a new cowl seal and will be installing it later today, hoping solve my problem!
Cables seem dry. Seal at the bottom of the door was dripping wet.