Fought the water accumulation on the passenger side floor for several years; the following were what I did during troubleshooting:
Cleaned the drain for the cowl air intake, sealed seams in the general area, ensured the evaporator pan drain was clear (several times), verified the foam surrounding the coolant and refrigerant lines were sealed and replacing the hood to firewall seal.
Inspected the windshield frame to soft top header seal (2 years ago) and found the seal to remain compressed (loss of pliability) after the soft top pressure was removed; I determined the seal to be the original seal so I ordered a new OEM seal (55395101 AC) at an online Jeep dealer for $235.
I would rather pay more for an OEM seal than purchase a knock off and find that it fits poorly and continues to leak.
The new seal was thicker, different rubber material and a larger lip overhanging the windshield frame. Installed the new seal ensuring to clean the windshield header surface thoroughly and the tabs were on top of the side window headers. Since then the Jeep has been in numerous HEAVY downpours here is Florida and the water leak has not returned.
Your problem may be different, but this is what worked for me.