I know this is an old post but I have a 99 with the same problems I talked to my local dealer, they contacted their Ford rep but he refused to do anything. You may want to check with ford. they have a 7 year cutoff where they still might fix things. I fell just outside of it. Otherwise my local body guy told me to just keep spraying oil in the drain holes on the bottom of the tailgate and doors to slow the rust. It's a horrible design and a common problem on these trucks.