If the rough idle comes and goes (intermittent), it could be the EGR. I just replaced the EGR on my 2001 F150 5.4L. When it got below freezing, the truck would stall as well.
"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."
The answer could be something as simple as water in the gas due to condensation, which happens when the weather gets hot. To test out that theory, you can get a couple of tanks full of gas at a quality station (not a convenience store -- Costco has good quality gas) and see if the rough idle quits after you've cycled through a couple of tanks to clear out the water. Or you could need a mechanic.
For an experienced opinion specific to Ford Explorers, go to this site:
http://www.explorerforum.com/
which bills itself as "the #1 resource for Ford Explorer owners since 1996." I checked the dates of the postings, and they're currently active, so it's not a dead group. Groups of this sort usually have professional mechanics or experienced owners who like to answer questions and know what they're doing.
Sign up for a free account and ask your question in the right forum -- look for something like repair and maintenance.
Be sure to list the year of your Explorer and give them as much detail as possible -- don't just say, "Why does my Explorer idle rough sometimes?" They need details like if the truck idles rough when it's warming up and smooths out after 15 minutes, or if it idles rough after it's warmed up when you're waiting at a light, or if you've done anything to try and fix it (like poured an STP jet fuel additive into it).
Good luck, I hope it's something simple.
Check throttle cable. A bad throttle cable will cause it accelerate
& decelerate. Check for worn out cable and replace it.
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