I had a similar issues with my 03, leaky windows, wrecked seals, etc. and when I traded it in I found out why. My car was ordered by someone from the dealership who wanted it for themselves and when it arrived they noticed the door gaps were quite large, they looked into it further and found the body wasn't sitting on the frame correctly. Ford took the car back, sold it to another dealer in the same city and that dealer leased it out. I bought it a year later and was never happy with the noisy doors.