Whenever it rained, I would notice my back seat was a little wet afterwards. I did some research online and found this to be a pretty common issue for 1997-2003 F150 owners. Here is a quick summary of how I fixed the leak. It isn't as hard as you would think. I recommend having a partner help you.
Instructions...
Remove the top of the seat belt, clothing hook, and back side panel from the truck. The side panel should snap off, but there are two clips holding it on so try to be careful not to break them. If I remember correctly, there are two caps in the headliner that pop out using a flathead screwdriver.
Now you are ready to work on the window. While removing the screws around the window, you will need to bend the headliner back a little. Only bend it back as far as you need to so you don't damage it permanently. You won't need to remove or loosen the seat, just pull back on the headrest and you'll see the screws.
After you are sure you have all the window screws removed, you will need to get a knife and scrape around the edge of the window (from the inside) to break the connection. After you cut around most of the frame, you should be able to push outward (apply pressure all over and not in one spot) and the window will start to come free. Have someone in your truck bed to hold on to the window.
After the window breaks free, scrape the rubber off the cab window frame. I recommend using a putty knife and
NOT a razor. A razor will peel into the frame itself, especially around the glass.
While your scraping the old sealant off the cab, your partner can be working on the window. Scrape the old sealant off the window as best you can, but if you scrape too hard or use a razor it can start digging into the frame.
After you have cleaned off the old sealant, you can apply your new sealant. I will post what kind I used later because I can't remember the name of it right now. I purchased it at Lowe's. Apply the sealant to the glass and I think it was easier that way. Don't apply it to the cab AND the window, or else you will have too much and it oozes everywhere. Don't get sealant on the window screws.
You and your partner can line up the window to the frame and just push it back in place. I recommend tightening the screws in a circle a little bit at a time (similar to what you do with lugnuts) so that the sealant is applied somewhat evenly. Reconnect everything and your done.
It took me about 2 hours, so if you know anything about fixing cars it should take you about half that. The dealers quoted about $200-300 to do this repair.