The plugs. Many people have had problems with Bosch plugs, although I must admit the problems seem to be with the Duratec. I don't have any experience with the Zetec.
I'd replace the plugs with the Motorcraft or Autolite recommended plug, especially since that's going to be the cheapest fix (as opposed to wires, coil, etc.). I had Splitfires in my Sport before I had a clue and the same kind of "miss" would happen at higher speeds. I'm sure if I had left the plugs in for longer I'd start seeing the miss at lower speeds, too.
Anyone with a Zetec that can correct me, please do.