My '99 also leaks from the rear slider window, passenger side. If you do a google search, you will find this is a common problem. There is a ford service bulletin on this problem:
*04-2-2***BODY - BACK GLASS - SLIDING BACK GLASS WINDNOISE/WATER LEAK - SEAL REPLACEMENT
I haven't gone down to the stealership and asked them about this yet. Other f150 owners have resorted to using a tube of silicone from the hardware store.
I'm not prepared to go that primitive, yet.