I had the simular issue last year. I added an auxillary tank in the bed and water was getting into that tank through one of the plugs on the tank. They just changed the sensor. I change the filters every 10K miles and I drain my seperator every month like clock work and have not had another issue. What Hub City Ford told me was to buy quality fuel at stations that sold large volumes of diesel where as it did sit in there storage tank for long periods of time. Do you use fuel additives? The motor craft additive is good just a little pricey at the dealer, I use the diesel Kleen made by power service at walmart in the gray bottle every other fill up. It is a cetaine booster and it lubricates the internals of the fuel pump and cleans injectors. But besides that I have not had any other issues with the 6.4 liter engine.
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