My truck is knocking when I first start it.

I ran through high water and imediatly after my 2007 Ford F-150 started to misfire and run ruff. I stoped for about an hour and it seemed th stop. But still every now and again when I push the gas it will still miss. Now when I first start the truck it will make a knocking noise coming from the engine. I checked the oil and that looks fine and is at the correct level. What could be the problem?