I'm in the same boat. We had a ton of rain the last week, and I have moisture where the jack stand is kept behind the passenger side (I have a 2001 Crew Cab). I've had this window replaced twice already for leaks. Last time, it was on the driver side, and now its on the passenger side. It was replaced last Christmas.

Originally I thought that maybe the camper shell with the large rubber boot was pushing on the glass, but when I put the shell back on, I made sure that it was just touching the glass. There has to be a permanent fix for this. I'm surprised that Ford does not have any fixes for this issue.