if the fuel filter replacement worked for a while, i would try draining the fuel water seperator or "fuel filter" housing. if you have a 7.3L it is on the top of the engine, partly under the plastic cover(the first thing that you normally see). it is a large cylinder with a strange looking cap look around the sides and you will see a small yellow lever that turns 90 degrees. it is the only wellow lever on the whole engine so you cant go wrong, just turn it.
if you have a 6.0L it is located underneath on the frame. look under the drivers side, on the frame, mounted just forward of the transmission cross member. you will need a 6mm allen wrench(use the short end) to take the plug out and let it drain.
if you have water in the tank it may take a few times before the problem is fixed.
a cmp sensor can cause those that type of thing to happen. it might be worth checking out to see if your vehicle qualifys for the recall (replacement) of that sensor.