Frenchie its not the door seals its the useless foam they fit to the hard top.
I have an aftermarket convertible roof for summer use and that as more substantial rubbers on the door surrounds. I have been through deep puddles and torrential rain and that doesn't leak. As soon as the hard top is put back I get water in my drivers footwell. I have sourced exactly the same foam rubber and I am going to replace it all myself (cant be bothered with taking it back to the dealer). I am just waiting for a nice day to do the job.
Pack of: 5 x Self Adhesive Peel Off - Black Foam Sheets 175mm x 135mm x 3mm | eBay
This is the foam I am going to fix mine with . cost £3.20 its worth a try.
Also theres a pdf from jeep telling you how to fix all the leaks I have it on my pc. its about 5mb ..its called jk-water-leaks-all. iI am sure its for download on here somewhere.