Had that problem, warranty was denied first by the dealer, then by the Ford customer dis-service hotline. They quoted $700 to do all the work, but Century Ford in Rockville really weaseled me before I caught on.
First they called saying I had rocks in the tank, it seemed to be vandalism. I go to the dealer to check it out, they hadn't even looked. So, I ask them to please look, but they charged me for 2 hours labor just to do that, I think $160. They showed some powdery debris caught in filters, but denied coverage because a few drops of water were in the tank. I found out later that under the warranty they had NO RIGHT to charge me money if they didn't know what the problem was. Bumper-to-Bumper doesn't cover non-warranty things like pieces getting broken and wear/tear, but it does provide for a free analysis to determine if something is caused by a manf. defect. If I were you, put a little bit of that stuff to remove water from the tank in there just in case!
To make a long story short, I "only" paid $400 to have them clean it but not replace anything. The problem kept recurring after a short time, so I took the extra step of dropping the tank and throwing away both filters that were in the tank. Didn't clean them, threw them away and didn't replace. No problems since then, although I probably should get a backup fuel pump and do the "hole in the back seat" mod that gives easy access.
