Check if you have any DTC's, engine fault codes. To do this, turn ignition on with-out starting, off, on, off, on and wait. Look at the odometer, it will flash any codes for the PCM and the ECM. This will hopfully point you into the correct direction.
After changing the fuel filter, if you have extreme trouble restarting, chances are the lift pump is dead or so weak that it can not pump fuel through the new filter and up to the injector pump. To see if the lift pump is working, find some place quiet and open the hood. Turn truck ignition on and just bump the starter without starting. Do not turn ignition off! You should be able to hear a wining noise coming from the drivers side back of the engine. If you do not hear it, chances are the lift pump is dead. If the pump is dying, it will sound funny, like the rpm's of the fuel pump is not correct or steady.
Hopfully it is not more than just a lift pump. Check for trouble codes.
-Rich