body leak

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I pulled up the vinyl carpet on my 05 to find rusty floors and water. Now I need to clean up that mess but more importantly I need to find the leak and yes I have a moon roof. Any ideas or suggestions?
 
@Les - the Gen 2 has the leaky third brake light. I do not believe that the Gen 1 had that issue.



@Frank - check the drain tubes for the moon roof under the headliner as that is most likely where the water is coming from.
 
I also noticed water stains in the back corners of the head liner between rear seat windows and the back slider. They don't seem to be wet now but have defiantly been wet before. I'm going to remove all the seats and console and vinyl floor covering and I was wondering how difficult it is to remove the console? Thanks for any help in this matter. I love this truck and don't want this to be the reason I get rid of it.
 
Gen 2 has the leaky third brake light. I do not believe that the Gen 1 had that issue.

Gen 1 third brake lights DO leak, just not as common. (See link below) Also don't rule out the roof racks.



 
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I've done quite a bit of investigation and I'm leaning towards the roof rack that is causing my leak. I found all of the screws to be less then snug. I tightened all of them and also checked the drains for the moon roof and found them to be clean and clear. I removed the 3rd brake light housing and found very little sign of moisture. Next I'm going to remove the entire interior and dry everything out then clean the floor the best I can and use the 3 step POR15 system. Hopefully this will remedy the situation. I know it's going to be a lot of work and it's going to require a few days drying time but like I said I really love this vehicle so it's worth it to me.
 
Just a suggestion, check the drain line from the intake air vents in front of the windshield. My 01 ST leaks. In a heavy rain, I get a slow drip on my shoes. I think the line runs under the dash over to the drivers door then down and out. I have yet to locate the leak but I've felt the water on my foot (I don't have a moon roof).
 
I completed the job and it sat drying for three days and then sat for another week inside my garage. Today it's been raining off and on so this will be a test and see if I accomplished ANYTHING at all or do I still have a soggy floor. Wish me luck.
 

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