One of the main issues I have with Ford diagnostics is that multiple parts could be causing he problem. and not just one, sometimes it's 3 or 4. I've had a rough idle on my GT for a while. I did a general tune-up first; replaced the spark plugs, plug wires, and distributor cap & rotor. I also replaced the coil and tfi module while I was at it. The idle improved but was not as smooth as it should be. So this weekend I replaced the pip in my distributor and re-adjusted the idle. Yet again, the idle improved but is still a bit rough.
My point is, several components could be contributing to the problem. Everyone's suggestions are possible causes, so you'll need to hit up one at a time and see if any of them help.