My 03 also used to set that light even after draining the housing and replacing the filters. I was told to remove the cover (the part with the 4 lines and the drain plug, ford calls it a fuel manifold) and clean the actual sensor with carb or brake cleaner. You'll need a new gasket (from the dealer) however. Make sure you dry it out good so no carb cleaner goes thorough the injectors. I believe the sensor is in the fuel manifold/cover. I pulled mine off, sprayed it cause it was full of some brown slimy stuff, blew it dry with compressed air, and reinstalled. That fixed my water light.
You just remove the 4 lines with the fuel line disconnect tool (available at most parts stores, kind of made like scissors), unplug the 1-2 wire connectors (depending on weather yours has the fuel heater) and remove the 4 bolts from the cover. Its been my experience that the fuel doesnt drain as long if the tank has a lower fuel level.