For months I've been trying to isolate the leak onto my front passenger floorboard and it looks like I've finally beaten it. There were two sources -

1. The cowling leak through the HVAC cold air intake on the right side beneath the cowl louvered panel was one. I had opened up an access hole (Dremel cut-off wheels) to get better access to it. I suspected the foam rubber used to seal the rectangular hole the intake protruded upward through might be a problem. With the new access hole I could manage to seal around that with silicone sealant. When I opened up the access hole the piece I removed to gain access had a spot-welded trough beneath it to channel away the water that leaked through the screws that hold down the louvered panel that normally sits above the area. That trough prevented water from leaking straight downward into the opening of the air intake. Suffice it to say my best efforts to reseal those two screws did not work and I was actually getting more water inside than before I applied the silicone sealant. Good intentions made matters worse. So, I fashioned a cover from aluminum flashing that slid over top of the air intake with sufficient clearance above it to allow it to breath normally. That little fix stopped most of the floorboard water leak. There was still water leaking inside but I could readily see from where.

2. The passenger side carpet was wet just below the kick panel along the lower edge. I removed the panel and found that the antenna wire rubber bung that seals the through-hole where it passes through the body from the fender mount location had come loose. I suspect that it shrank over the years and was no longer able to fit and seal tightly in the through-hole. That hole was where the water was entering as it ran down from the cowl area as it normally does. The bung would sit in the hole but a slight tap and it would fall into the void between the body and fender. I used a generous fillet of silicone sealant around it to re-secure it. Additionally, I had lost radio reception some time ago and blamed it on a failed antenna. When I removed the kick panel I found that the bayonet connection between the antenna coaxial wire and the radio had failed due to corrosion from water exposure. Bonus: I fixed that too and got my radio reception back.

Summary - Knowing what I know now I would conclude that the original leak was probably due to the antenna bung slipping out of the hole allowing water run-off from the cowl area to enter the passenger side.

Areas inspected that were not the source of the leak --
1. The fan gasket on the firewall.
2. The horizontal body seam at the hood-to-cowl rubber seal.
3. The windshield seal.
4. The firewall through-holes where various clamps and fasteners are located.
5. Other body joints where the cabin meets other body structures - a) where the inner fender structure meets the cabin, b) the joint inside the cowl beneath the windshield lower edge.
6. The passenger door jamb where the wire bundle rubber boot is secured.

Being a 96, the fuse panel is located beneath the driver's side dash. Had this leak been on my 98, where the fuse panel is on the passenger side kick where the leak was found, I'd have had a much more difficult time accessing the area to inspect for the leak and make the fix. It would be easier to remove the right fender on the 98.

 

Yep. I bought mine (98) with an aftermarket antenna. One of those little rubbery short ones. It didn't have the rubber seal on the wire. It rained inside all the time. I didn't care, it's a Jeep. It's supposed to get wet inside insideUntil the day my interior lights wouldn't turn off. It corroded the power distribution center. Bad. While I was down there, I found how soaked the carpet was so I pulled it back and found a ton of rust.

Moral: Don't let it get wet. And if it does, don't let it stay wet.