I have a 99 Extended cab that had multiple water leaks. Here is what I did to repair them.
First, I was getting water in the passenger side rocker area after a hard rain. After removing the rear seats, rear trim and carpet, I had an assistant hold a garden hose over the back window and roof while I looked for the leaks.

Leak 1: The sliding rear window was leaking from the center section. There is a seal that runs the length of the sliding portion that had shrunk over time. This seal is on the top and bottom of this sliding portion of the glass. It has shrunk so that the sides of the seal no longer contacted the window frame. This caused an excessive ammount of water to leak past the glass and into the sliding window track and overflow down the back of the truck and ran down to the floor. To fix it, I removed the top seal and cut a small section from it to fill in the space of the bottom seal. The seal can be removed by opening the window and pulling it straight out. Then reinstall the top seal and blow out the sliding window channel on both sides. This seal is not a water tight seal and some water will leak past it. There are drains in the channel that go through the rear window seal. These drains are located in the area where the two body depressions are on either side of the truck below the rear window. Make sure these drains are cleared. The top seal will now have a larger gap in it but that will not cause a problem because the water will run down the window and not collect at that seal (unless your truck is upside down).

Leak 2: Both rear cab vents were leaking where they seal to the body. To remove them, I depressed the plastic tabs and pushed them toward the bed and released the clips. Then I was able to tilt them at an angle and pull them into the cab. Others have suggested to slide the bed back but it was not necessary for me. Your results may vary. Remove all the old sealing foam and glue, and install a small bead of glass setting butyl tape around the vents and reinstall them.

Leak 3: There was also a leak at the body seam sealer just below the passenger rear window drain that was mentioned in leak 1. I used silicone sealer to seal up this leak from the outside. Just be sure it is paintable or the same color as your paint.

Leak 4: Water was leaking into the blower motor housing and onto the passenger floor through the recirc./fresh air door behind the glove box. The easiest way to fix it was to drill two small drain holes into the housing. Do this from underneath the truck on the engine side of the firewall. You may have to remove a few screws from the fender liner to access the blower housing.

I will try to post some pictures on here as soon as I figure out how to.

Mabye others can chime in and add other repairs for the other areas that are prone to water leaks on these trucks to make this a helpful thread.

 

Thank-you for this info. It was helpful. I did drill a hole in the blower housing to drain lots of water.

Oldforddy

 

why drill holes in the heater box when there is a huge drain hole built in?