I have a 2012 Jeep 2dr JK hardtop that had water leaking thru both door seals. This allowed rainwater to flow into the footwells during every storm. I took it to the dealer and they tried various factory "fixes" but to no avail. This problem was eventually fixed it by replacing both door seals.
I thought I would post the solution to my problem in case any of you have encountered "soggy" footwells in your vehicle. I'm not saying this will be the answer to your problem but it is something to consider.
The first photo shows the area leaking and the faulty door seal. The seal was made such that when the door was closed it left a gap that water could run down behind the gasket (a portion of the seal can be seen sticking thru the door space). Since the roof gutter drained right into this area water can easily fill the footwell.
The second photo shows the same area mentioned in the first photo but the new seal fit tight against the door opening and left a channel for the roof runoff water to exit down the outside of the seal and harmlessly away.