Just Came across this in the February 2012 issue of Motor Magazine and thought that I should share this as this is a very common thread here on the FTE forum.

"Owners of some 1997-2005 Ford Trucks with the 5.4L two-valve engine may complain of an intermittent rough idle. One likely cause, says Ford, is noncommanded EGR flow. A stuck open EGR vlave is ultimately the culprit.

To make a definitive diagnosis, connect your scan tool, start the engine and allow it to reach normal operating temperature. Next, allow the idle to stabilize, scroll down to the DPFEGR PID on the scanner's display and write down the voltage. Now disconnect the vaccuum hose to the EGR valve and connect a vaccuum pump to its port. Pump the vacuum up until the EGR valve is wide open, then bleed off the vaccuum. Record the DPFEGR voltage again. Repeat this procedure several (about 8) more times.

If the DPFEGR voltage increases by .03 volt or more from the initial reading and the idle gets rough, the EGR valve is probably stuck open. Try tapping the casting with a wrench. If the voltage decreases and the idle now gets smooth, the valve is definitely sticking. Replace it with a revised design, Part No. XL3Z-9D475-CA.

Trucks that can benefit from the upgraded EGR vlave are 1997-99 F-250 light duty pickups, 1997-2004 f-150s, 1998-99 Lincoln Navigators, 1997-2005 E-series vans, 1998-2004 F-super duty pickups and 2000-05 Excursions."

-Tom Rosario (Feb. '12 Motor Magazine - "Service Slants")