2002 Ford Truck hesitation on 5.4 V8

I went duck hunting two days ago and had to drive through a few water holes where it ran fine when I shut it off to hunt, after we were done I started the truck to leave and it was running rough as though it was missing. The truck would shutter as I accelerated and when I let off of the gas it would stop. It would also smooth out if I slowly pushed down on the gas pedal, but if I pushed it down to accelerate more it would shutter until I let off the pedal. I let it run for almost six hours trying to dry it out for I figured something got wet but it is now three days later and it is still doing it and even worse it seems. I do not have a scan tool to see what codes it has thrown, so I am looking for whatever advice you can provide. Thanks in advamce.