Rear Cargo Subfloor Cavity - Water Pooling?

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One additional insight/discovery:

While the 3rd brake light was the main problem, after my temp silicone fix (going to switch out to new later), a smaller leak persisted in the same area.

Chased it to the tailgate wire run. A few years ago I had a backup cam installed, and they ran the wire through here. Camera wire had separated from the other wires and is sitting outside the conduit, and popped the rubber seal thing up, allowing water to trickle in.

I reseated the rubber thing (technical jargon), which doesn't feel like a bulletproof solution but stopped the drip. If anybody has better solutions I'm interested.

PS - never have Best Buy install anything.

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I stripped the entire interior except for the dash looking for the water leaks that drenched the 2nd row carpet and the rear from the 3rd row seats back. leaks. I now know I had three leaks: 1.) the 3rd brake light was cracked and leaking. 2.) The LH roof rack rear bolts. 3.) Sunroof glass seal. I had over an inch of water in the rear body bolt access holes and almost 1/2" in the rear and 2nd row floorboards. I replaced the 3rd brake light with a new OEM unit a couple weeks ago.

Tomorrow I will try to remove the LH roof rack and see what is needed to seal up the bolts. My big concern with the roof rack R&R is the trim pieces around the mounting base of the roof rack. As one time they were flexible. But due exposure, they are now brittle and faded white. I'm pretty sure they will crumble when I try to remove them. Anyone have any suggestions. I have a 2000 LX470...are the later model year roof racks compatible? I know the design changed in the later years and they appear more durable.

For the sunroof leak, I will most likely have to replace the seal. But, I was going to try to apply weather-strip adhesive or some other type of sealer to see if I can patch it. It's leaking right from the center rear of the sunroof where the seal ends meet. Unfortunately, the drip is not caught by the drip pan. Anyone had success sealing a leaking sunroof seal between the glass and the seal?

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I replaced the weatherstripping around my sunroof (it was super worn out—white and actually frayed at a couple places) and sealed it with 3m weatherstripping adhesive.
Noticed a leak (actually my kids saw the drip from their backseat perches) a couple months ago. Ran a bead of 3m adhesive around the plastic/glass junction. Reduced but not eliminated the drips. Squirted captain tolleys leak stop stuff all around the same junction—it’s really liquid and finds leaks well. Sealed.
 
Just a recommendation, if you want to seal the 3rd brake light the typical product to use is some butyl rope. There is a post about it in here somewhere, but basically you pull the light out and use the rope to seal around the housing and then reinstall it. Easy job, just two bolts from the inside to remove the light.

Butyl rope is the best! However I think you’re underselling the elbow grease involved in getting the old adhesive off. Took me forever! 😂

2 minutes to remove the light. 2+ hours to remove the old seal residue.
 
Butyl rope is the best! However I think you’re underselling the elbow grease involved in getting the old adhesive off. Took me forever! 😂

2 minutes to remove the light. 2+ hours to remove the old seal residue.
Yea my partner would tell you I am notorious for that. She will ask how long something will take and it’s always five minutes lol. Trying to get better.
 
This forum is just insanely helpful, so here is a small attempt at paying back with my roof leak experience.

First, thanks to @neoworm and @awesomeissquid for their posts here. Super helpful. In some other post there was a reference to the GE silicone; thanks to that poster, too.

When I got the headliner down for a sunroof repair, and got a car wash, it was like I was in a submarine with a screen door. So depressing.

1. As the OP (@Gnarwgn) discovered, first check your third brake light. Mine was an absolute gusher running into the subframe. Small ponds were forming.
2. My roof rack bolts were leaking too, but don't sleep on the *other* 6 bolt hole roof penetrations. This was the root of my problem. You can expose these by removing the cosmetic longitudinal weatherstripping that covers the drainage channels. There is another great post on removing those here: Removing Roof Drip Moulding - https://forum.ih8mud.com/threads/removing-roof-drip-moulding.1238901/ This is where the butyl tape idea seems to make a lot of sense vs. the cardboard-type OEM washers.
3. Carefully inspect the welds in the drainage channels. There was a tiny slit in one just fore of the middle rack mount that allowed water to run right down the inside of the B pillar and onto the rear passenger seat belt reel. I put a bead of silicone over it and problem solved, but I expect this one to reappear.

I think the best tip to offer is: once you go through the trouble of taking down the headliner, keep it off for a while and spend some time getting a few car washes or putting it under a sprinkler. These things leak. Luckily my rig was seemingly garaged quite often, as the headliner shows zero water marks. If you keep yours outside or live in a rainy climate (or both), the headliner could be hiding some issues you will want to deal with.
 
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This forum is just insanely helpful, so here is a small attempt at paying back with my roof leak experience.

First, thanks to @neoworm and @awesomeissquid for their posts here. Super helpful. In some other post there was a reference to the GE silicone; thanks to that poster, too.

When I got the headliner down for a sunroof repair, and got a car wash, it was like I was in a submarine with a screen door. So depressing.

1. As the OP (@Gnarwgn) discovered, first check your third brake light. Mine was an absolute gusher running into the subframe. Small ponds were forming.
2. My roof rack bolts were leaking too, but don't sleep on the *other* 6 bolt hole roof penetrations. This was the root of my problem. You can expose these by removing the cosmetic longitudinal weatherstripping that covers the drainage channels. There is another great post on removing those here: Removing Roof Drip Moulding - https://forum.ih8mud.com/threads/removing-roof-drip-moulding.1238901/ This is where the butyl tape idea seems to make a lot of sense vs. the cardboard-type OEM washers.
3. Carefully inspect the welds in the drainage channels. There was a tiny slit in one just fore of the middle rack mount that allowed water to run right down the inside of the B pillar and onto the rear passenger seat belt reel. I put a bead of silicone over it and problem solved, but I expect this one to reappear.

I think the best tip to offer is: once you go through the trouble of taking down the headliner, keep it off for a while and spend some time getting a few car washes or putting it under a sprinkler. These things leak. Luckily my rig was seemingly garaged quite often, as the headliner shows zero water marks. If you keep yours outside or live in a rainy climate (or both), the headliner could be hiding some issues you will want to deal with.
I've been to the mountaintop. There are no more leaks in my roof. Thought I'd add some more tips in hopes of helping others.

4. With the rack off, take a close look at your *center* rack cushions. One of mine had some kind of deformity that let water through a penetration with no bolt. (Side note: by my count there are 18 roof penetrations on this vehicle: 12 for the rack (10 bolts, 2 protrusions from the middle rack cushions) and 6 for the rest of the frame. There has to be a better way.)

5. Maybe I was doing it wrong, but siliconing the old bolts proved less effective than buying new OEM ones with that green goo at the tip. They are $1.66 each. For $16.60 this seems like a no-brainer. Just get new bolts.

6. Don't give up. Several times on this journey I was ready to quit and accept some leakage. Don't do it. There are 18 roof penetrations, plus whatever bad welds you've got. Everything can be plugged up with enough effort.

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