2005 Ford F-150 fuel pump/coil?

Hello-
My husband had his truck into the repair shop a few months ago because it was running rough intermittently and the engine light came on. They ran it on the diagnostic coming back with a misc code. Changed the fuel filter and decided it was the ignition coil, which they changed. The truck has been running beautifully. He just returned from a 2000 mile trip which it ran great. It is now back to running rough with the engine light coming on. When he describes it to me it sounds like a clogged fuel filter, but it was just changed. Should we change the fuel filter again and could it be the coil again? If it is the coil, what might be causing it to fail so soon. Thank you for your time- Cindy Wright