Just went through the same thing, it starts off small, and then gets worse. It will eventually throw a service engine soon code if its misfiring bad enough. Once it does, you will have a pretty good idea what it is. I bet you have a bad plug or ignition coil (COP), but until it codes, it will be hard to know for sure.
2001 F50 XLT 4.6l V8 Supercrew
w/Rhino Liner, Undercover Tonneau, Billet Grille so far