2005 TJ hardtop gaps around doors and tailgate

I'm not going to mess with those tailgate hinges until I decide to upgrade them, given the horror stories. I think mine has a slight sag after 16 years despite only holding a stock tire.
 
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An update since I spent a good chunk of time this weekend working on this. I did a bunch of things:
1) Removed the hardtop and replaced all the weatherstripping. I used some adhesive backed weatherstripping I got from Home Depot for this.
2) Installed the mucket seals on both sides while the hardtop was off
3) Adjusted the tailgate with a detour in broken-bolt hell and a few other minor problems.
4) I ended up just adding 2 strips of foam weather stripping where the liftgate glass lands to close the gap. I adjusted it as much as I could and there was no getting it any closer. I'll just replace this yearly.

We had a good amount of rain most of today and so far I'm dryer. I found one remaining leak coming from the firewall between the engine and passenger side. Here is a wide shot:
View attachment 210449
And here is closer up on the opening and parts going through.
View attachment 210450

I *think* is part of the HVAC system but I'm really not sure of where the water is getting in. If the water was coming through the engine bay I'd expect to see drips from the unsealed hole to the right in the above picture. Note that the car has not been driven today so no splashes are involved with these leaks. Two weeks ago I did clean out the cowl drain and noticed that there is a gap between the metal and the cowl drain itself. Water drained through both openings after I cleaned it out. It did not *look* like water was going anywhere problematic when I was testing.

Any suggestions on where to go next?
I took off the air intake cover that’s inside the cowl and did a bead of silicone around it to seal it up nice. Once you do that water has to get pretty high inside there to leak down in.
 
An update since I spent a good chunk of time this weekend working on this. I did a bunch of things:
1) Removed the hardtop and replaced all the weatherstripping. I used some adhesive backed weatherstripping I got from Home Depot for this.
2) Installed the mucket seals on both sides while the hardtop was off
3) Adjusted the tailgate with a detour in broken-bolt hell and a few other minor problems.
4) I ended up just adding 2 strips of foam weather stripping where the liftgate glass lands to close the gap. I adjusted it as much as I could and there was no getting it any closer. I'll just replace this yearly.

We had a good amount of rain most of today and so far I'm dryer. I found one remaining leak coming from the firewall between the engine and passenger side. Here is a wide shot:
View attachment 210449
And here is closer up on the opening and parts going through.
View attachment 210450

I *think* is part of the HVAC system but I'm really not sure of where the water is getting in. If the water was coming through the engine bay I'd expect to see drips from the unsealed hole to the right in the above picture. Note that the car has not been driven today so no splashes are involved with these leaks. Two weeks ago I did clean out the cowl drain and noticed that there is a gap between the metal and the cowl drain itself. Water drained through both openings after I cleaned it out. It did not *look* like water was going anywhere problematic when I was testing.

Any suggestions on where to go next?
Water in the passenger footwell is a common plague.

Pull the cowl off and see if there is any trash in the HVAC intake. Usually something causes the drain to get plugged and the water runs behind the firewall.

Usually that fixes it.
 
I think I found the source of the water. The wiring for the side lights and lightbar were jammed underneath the engine hood rubber weatherstrip which created a nice path for water to drain right down the firewall.

I'm starting to think I'm going to be re-doing everything the prior owner did to this Jeep... but this time not doing a hackjob.