I had this issue recently and after Ford thought they fixed it, probem came back. Pulled the COPs and 3 plugs were loose, just replaced them with new ones. I'd start with plugs first as it costs $0 to pull them and visually check.
On the same note, Ford really sucked when it came to figuring out the problem. I thought they could see which cylinder was misfiring and go from there as my Scantool software has this function to monitor individual cylinders but I need the Ford specific PID add-on but that's more $$.
edit: hey jpplaw, coud you expand on the alternator causing a misfire. Mine has a big load on it and knowing this could be helpful in the future if another misfire occurs that can't be tracked down. And it could be helpful for SYNY5TER to know. thanks!
Last edited by Ricardo; 06-30-2013 at 12:55 PM.