I had the same problem on my e350 7.3idi and changed the fuel filter but it returned, turned out i had to change o-rings on the injectors and replace the return caps and new fuel return lines, have not had any problems since,
But your problem could be the fuel tank selector valve, fuel filter bowl leaking air or the sealing o-ring on the fuel filter, if not check the fuel return caps for leaks or moist, it could be the o-rings on the injector or the return lines.
That is the most common cause usally, due to the heat and diesel eating away at the orings