You folks may be starting down a long frustrating road. Unfortunately, it is a road I know.
RJ2, now is a good time to do a little sound proofing if you're interested in that.
GSI has several products that you could use instead of the jute. More expensive, but really quiets down the ride. I would keep whatever you use off the low channels on the sides of the cab. Don't be surprised if after you fix the 3rd brake light the water keeps coming. I think there are as many faulty rear windows (backlight) to blame as there are brake lights.
R Butts, my window is at fault too. I've tried sealing that thing every way you can imagine including having it pulled out and professionally resealed, still it leaks. I'm about to buy a new aftermarket unit only because the Mopar replacement is over $400.
There are three TSBs (that I've found so far) dealing with the backlight: 23-27-97, 23-13-98, and 23-036-02. Look on
Fritz's info site for full details. A good tip I got last fall when I started down this road is to tape up your return vents for the HVAC in the door jambs, turn your vent on high, shut doors and windows, walk around cab with a spray bottle of soapy water. You'll get bubbles at your leaks. My third brake light doesn't bubble a bit, but man that backlight goes crazy. Mine is a slider and I think, at this point, it's designed to leak a little into it's drain channel. The problem is that the drain channel is channelling into the cab instead of to the outside. That's after about 6 months of fiddling with it trying to hold on to the hope that it could be fixed. I'm afraid I'll be spending this month's bomb budget on a new window, how lame! Sorry for the length, I've got some time invested in this particular problem. Good luck to all.