hmmmm... i know that my rear barn doors leaked really bad, i changed out the weatherstripping and that solved the problem. i don't know about the hatch style back, don't know how prone to leaking they are. another thing it might could be is the sealant for the body seam where the floor meets the fender steel. all those body seams are just spot welded seams with that urethane or whatever they put to seal them up. i'd read somewhere that if you had water back there it was a possibility. or maybe the rear window, which i would doubt, or maybe even the tail light. i know it sucks to say, but you may need to pull that panel off and figure out if it's coming in from slung-up water off the tire, or from water coming in from running down the truck. i looked at your install pics, i see that you have your air tank mounted and stuff already, but i might be best for you to pull that tank and panel off, and find out where that water is coming from. it's funny what you find when you pull those panels off. i didn't realize my cowl was leaking on the passenger side until i pulled the carpet out of my truck to fix the water leak i knew i had on the driver side. while i was at it i found out my barn doors were leaking like a sieve. (anyhow, that's another thread, not gonna bore you with it...) anyhow, you never know what's lurking under the carpet and such until you pull it back. luckily where yours is isn't probably too bad to get to, not too many panels to pull off. but i'd pull that stuff back out and try to find out exactly where it's coming from. if you find that it's a body seam, just go to the parts house and get some windshield sealant, the 3m stuff or equivalent that they use to adhere the windshield in when they install them. don't use silicone caulk, it can cause rusting later on. but that would be my vote, either the body seam where the inner fender steel meets the floorpan, or maybe the rear seal on the hatch/tailgate. just sucks that there's several things that it could be, just don't know how much it is beyond a shot in the dark until you get those panels off and find out if it's run-off water from the top, or splashed up water from below. sorry if i couldn't be more help, i definitely feel your wtf on finding water in your truck.
---------- Post added at 04:11 AM ---------- Previous post was at 04:09 AM ----------
i have a 4 door btw, maybe someone 2 door has some more insight or 1st hand experience on this