3rd brake light is a common leak issue with these trucks. I think most guys just reseal it with RTV or something similar. If you want to spend the money, the seal PN 20998779 is available. MSRP $18.32. It looks like the carpets are already out, so spraying to verify would probably be a good idea.

 

The seal on my 08 was bad, so I replaced with the factory one. It didn't last two years - I then used some foam weatherstripping from Lowe's or Home Depot and that is still going strong after five years... But that was not where my leak was coming from. I've never heard anyone else have this problem, but I had a pinhole at the very back of the roof under the plastic trim on the cab roof!

 

Cart knows what he is talking about

 

I used some 3/8" foam weatherstrip on both of my trucks. The '09 because it was leaking and the '12 just because I knew it would have to be done sometime.

 

Thanks guys. I did a search after the fact. I usually search before i post
i'll work on the 3rd light.
I hope it's not a hole or leakage on the roof between them black rails

 

Your picture makes me think it's the third brake light leaking. You should be able to see water inside of the lens or a high water mark of some kind on the inside of the lens. I would recommend if it is leaking to replace the whole assembly as the design of the lens is prone to splitting and gapping as they age and GEN1 trucks are old in years. You can get a pretty neat LED lamp for around $25 with the gasket included.

 

Had the same problem with my ‘07 Canyon. Got a led replacement that had a good closed cell foam gasket. That, and a lot of RTV, cured the leak.
With everything out of the cab you have an excellent opportunity to inspect all the of the floor for leaks or rust, clean all of that 17 year old dust and grime out and deep clean your carpet. clean the seats and trim well and you’ll be surprised how much better the truck feels and smells.