I'm fairly certain the biggest contributor to my leak is the 3rd brake light.

 

Where do you think it is getting in from? I sealed up the edges of the hinges, and the exposed bolts too.

 

From around the 3rd brake light. It's just a little foam strip around the edge of the plastic light so I feel like it probably has gotten rotten in 20 years and started leaking

 

Thats confusing me there. How could it be that? My 3rd brake light is on my hatch. Its not leaking in my hatch. Just the back part near the wheel well n inside near the tailight area somewhere.

 

I actually had the same problem. I just tightened the screws a little and it stopped. It was coming out of the molding at the top over my spare.
Thing is water travels. Going to assume it flows down hill, takes the path of least resistance, and comes out where it can.
The distance from where it comes in to where it comes out could significant.
So in your case to think it is leaking through there, going towards the passenger side, coming down that pillar, into your tail light/cargo area is
not out of the realm of possibilities. I can't remember how it is set up in there but if it were me (maybe there is just no way the water could travel
like that), having the tough time you are with this, I would investigate it.

 

Have you closely inspected the seal around the window above that wheel well?

 

I still dont understand. My xj has the 3rd brake light on my hatch. It is completely separate from the truck isealf. I doubt its that. Ive sprayed this thing on the roof, wit the hatch open! So its nowhere the 3rd brake light.

 

Both seals were replaced! After they were. Sprayed it with the hose to test it out and this nightmare began. Thought the seals were junk so the windows are sealed with Lifecaulk. A marine sealant.

 

Where do you think the wiring from the 3rd eye comes from?
Inside the Jeep of course.
Like I said my first leak was coming out of that upper plastic piece in the back of the cargo area.
Was dripping out the end on the driver's side on top of my spare tire cover.
Just tightened the screws a little and that stopped.
So I have to go with that is was the 3rd eye not being screwed down quite enough causing this.

Not saying it is causing your problem here but you can't figure it out
so it is time to start expanding your search.
Or as I like to refer to it as "reaching for straws".

 

I was gifted a 98 the owner threw his hands up on because he was at a loss as to how to repair the rust he encountered when he stripped out the interior of the truck (Classic, 4.0). What I inherited -

1. The right rear pillar that forms the right vertical lift gate seal was rotted through and the lift gate support rod bolt area was gone completely.
2. Both right and left rear corners of the roof were rotted away leaving holes approximately 8 inches front-to-back and 6 inches wide from the gutter inward.
3. The aft well area of the right rear wheel housing was rotted on the inside leaving a hole about 10 inches high and 3 inches wide.

I repaired the pillar by completely replacing it with the factory body panel original. The extreme top and bottom areas of the original were in good condition so I cut away the rotted section, matched and cut the new section to fit and then riveted it in at the liftgate seal bead (with sealant between the panels before joining) and otherwise bolted in in place. The rest of the repairs were done with fibrerglass. I had to reshape the contours of the roof aft corners. That took a bit of time to do. Then I wet sanded the roof, primed and refinished it.

While preparing the roof for paint I noticed two small paint bubbles where the roof curves down to meet the gutter in identical spots on the left and right sides. They were right about midway between the front and rear doors. These turned out to be holes. I ground away the paint and revealed rust that extended 4 inches fore and aft of the holes which ultimately ended up 1-1/2" in length, 1/4" wide after clean-up. I glassed both sides and then began checking the rain gutter more closely to find various small pinholes where water was entering the roof, collecting in the running trough of the interior roof structure and flowing either aft or forward depending on the pitch of the truck when parked or its inertia when moving. I repaired them all, which added an additional few days to my scheduled completion date.

After I was sure I'd uncovered and repaired all of the spots water was entering, I began wet sanding the roof with a slow running hose on the roof. One evening I noticed the driver's door window control was wet. I looked up and noticed a drip of water formed on the window plastic molding at the upper left corner of the windshield. This meant a window seal leak at the top where the hose water was flowing. I bought some black silicone sealant in a calking gun size cartridge and, using a plastic tool, lifted up the rubber seal surrounding the outside of the window and injected the silicone sealant enough that when the seal was released it would cause squeeze-out. I did this all around that seal cleaning up the squeeze-out as I progressed.

The net result of the long-term roof leaks left both driver's and right front passenger floor pans riddled with holes. I ground all that down, above and below, and fiberglassed it above and below. New carpet was installed.

I refinished the lift gate off the truck and installed it. After about a month of normal use I noticed the cargo deck was wet. I took a narrow strip of stiff paper and closed the gate on it. I was able to pull it out with little effort. I adjusted the liftgate catch on the bottom of the cargo deck all the way forward with no discernible change. I could still remove the strip of paper with the liftgate latched. I removed the catch and elongated the holes (forward) with a carbide burr on a die-grinder, re-positioned the latch and closed the liftgate. It latched and opened normally but I could not pull out the strip of paper. That repair, and the repaired holes I found and mentioned above stopped water from entering the truck.

 

thank you for the suggestion! I am going to look into this very much too. Right now i had to take a break from this leak situation. I wanted to get going on the lift, and sye after that so right now im going to do that. Sometimes taking a break from it, and starting fresh, the answer might be staring me right in the face. I will most definitely get back to this and keep you informed of whats going on!

 

I'm having the same issue just got the Jeep and it's obviously been happening for a while what was the end result on how you fixed it?