I've had a similar problem over a few years. Changed O-rings on the caps, covered them with plastic bags when kept on the lift. Inspected the tanks externally, they look near perfect on the tops for sure. Corrosion on the sides or bottom would cause fuel leakage, not water entry. (bilges are dry) Only two sources left are water in the fuel as received from the pump or condensation. I checked for water at the gas pump by filling my portable 28 gallon tanks, letting them sit, and sampling them. Never found any water that way. However, after high humidity conditions, I would occasionally get "water in the fuel" warnings from the F250 engine filters. I run each engine off a separate tank (Starboard engine=Main 195 gal tank, Port engine=Aux 150 gal tank) I have had warnings from fuel supplied by both the tanks and found up to 16 ozs of water in the separators each time. Once I clear it up, I may not get another warning for 6-12 months. With two boats, I only run the Grady 75-100 hours per year. Seems to occur more on hot, humid summer months. I carry two spare yamaha fuel separators (the larger ones) and a glass jar on every trip. My theory is condensation. Larger, less than full tanks, are more prone to the problem. I've seen similar problems with aircraft fuel tanks, but they are usually drained from the low point after sitting for any length of time. If I keep the tanks full, it seems to lessen the problem but 350 gallons of fuel is a lot to carry around on short hops.