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before you go nuts on the window make sure it is the window with a 2 part test. Get some of that nonmarking painters tape and clean the area around the top of the window. Tape it up and hose the window and the rear brake light. Then take the window tape off and tape up the brake light and hose again. Recently discovered that my leaking rear window was actually the brake light seal.
the window will push out, just use gentle pressure over a wide area. It makes a mess to clean up all that goo. It will take an hour + just to clean the factory rope "goo" gasket properly.
I just bought the truck and I was cleaning it out and I noticed the driver side floor board was soaked and the passenger side was damp. The head liner has some water stains by the window. It also looks like someone put some sealent around the third break light.
Again, before taking that back window out, confirm where the leak is coming from! Mine was dripping on both sided only in heavy rain at the corners of the rubber window gasket. Its possible, though not very likely that it can be 1/4 windows if its an extended cab. The third brake light seems to be a constant source of leaks on these and the f150s from what I can tell. Good luck and let us know what you come up with!
edit:
when I got my truck it had a broken out rear window. I replaced it with a solid window and used rubber silicone. Leaked and leaked. Figured I did a bad job. Got proper rope gasket, basically ford replacement, pulled window, resealed it. Guess what? Still leaking. Did the tape test and have realized it was the brake light. Used strip caulk as a temp test for a few weeks. Now need to come up with a perm fix. Spent a lot of time and headache! Just want to make sure you dont waste your time with that window if thats not it!
Ok I found out where the water is coming from! I poured a bunch of water in the cowel panel and I watched the water stream in. I have the carpet pulled back now. How do I fix this? You can't remove the cowel panel and can't see anything
Oh, so its from the front? That I have not dealt with so cant help you. i do know my pass floorboard does get wet from time to time. I had the front window replaced by a professional and figured they screwed it up. Guess I need to test mine now!