I had the same exact issue you are experiencing with my Mercury 9.9 4 stroke which was hooked into my main fuel tank. I first replaced all the hoses and the primer bulb and the fuel filter it helped a little but it still happened every few hours. The next thing i did was replace the fuel pump and that alleviated the issue. What i think happened on my 2000 kicker motor the fuels filter diaphragm was compromised by the alcohol in the fuel and that where i think i was losing prime. Since i replaced with a new fuel pump that is compatible with ethanol gasoling i have not had the issue since.