4.6l. After warm-up, why does it run rough with missing?

Clean the Throttle Body and Mass Air Flow Sensor. Also check for DTCs (diagnostic trouble codes).

..

It can be issue with IAC( idle air control valve) causing the problem.

There are many other possibilities causing these idle issues. Engine idles rough.

There are few help links with solutions to troubleshoot such idle issues.

I suggest you refer the link below and follow its troubleshooting details:------

Click the link below:-----

Ford Expedition IAC valve replacing

http://technoanswers.blogspot.com/2012/12/ford-expedition-iac-valve-replacing.html

Bad miss at idle?

http://technoanswers.blogspot.com/2012/01/bad-miss-at-idle.html

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Stumbling and stalling at idle after engine rebuild?

http://schematicsdiagram.blogspot.in/2012/03/stumbling-and-stalling-at-idle-after.html

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1999 Ford F-150 Idles rough and quits when gas pedal is pressed less?

http://technoanswers.blogspot.in/2012/01/1999-ford-f-150-idles-rough-and-quits.html

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Engine stumbles coming off idle when warm?

http://repairhelpcenter.blogspot.com/2012/01/engine-stumbles-coming-off-idle-when.html

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Erratic idle on car?

http://schematicsdiagram.blogspot.com/2011/12/erratic-idle-on-car.html

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Cold start problem and vehicle shudder around 2500 to 3500 rpms

http://repairhelpcenter.blogspot.com/2012/10/cold-start-problem-and-vehicle-shudder.html

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Low idle when cold out side?

http://repairhelpcenter.blogspot.com/2011/12/low-idle-when-cold-out-side.html

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GMC Sonoma Stalls and idles low

http://technoanswers.blogspot.com/2012/10/gmc-sonoma-stalls-and-idles-low.html

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GMC Idle Air Control (IAC) Valve Replacing?

http://schematicsdiagram.blogspot.com/2011/12/gmc-idle-air-control-iac-valve.html

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1996 Camry intermittent engine failure while idle?

http://repairhelpcenter.blogspot.com/2011/10/1996-camry-intermittent-engine-failure.html

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Engine quits at idle?

http://repairhelpcenter.blogspot.com/2011/10/engine-quits-at-idle.html

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Car overheats and Air blows hot at idle?

http://howtobyme.blogspot.com/2011/11/car-overheats-and-air-blows-hot-at-idle.html

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High Idle Problem

http://repairhelpcenter.blogspot.com/2012/10/high-idle-problem.html

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While stop engine idles like cylinder missing?

http://schematicsdiagram.blogspot.com/2012/01/while-stop-engine-idles-like-cylinder.html

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Idle flair is noticed on car? Rough idle? car will not idle? Erratic idle speed?

http://technoanswers.blogspot.in/2012/02/idle-flair-is-noticed-on-car-rough-idle.html

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High rpm in neutral? Inconsistant high RPM in neutral?

http://technoanswers.blogspot.in/2012/02/high-rpm-in-neutral-inconsistant-high.html

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Vehicle stumbling at idle and shows code 54?

http://schematicsdiagram.blogspot.in/2012/03/vehicle-stumbling-at-idle-and-shows.html

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Rough idle, staling and Erratic shifting?

http://technoanswers.blogspot.in/2012/03/rough-idlestaling-and-erratic-shifting.html

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While stop engine idles like cylinder missing?

http://schematicsdiagram.blogspot.com/2012/01/while-stop-engine-idles-like-cylinder.html

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These details will help.

Thanks.

For rough idle issues and problem troubleshooting,go through the help links provided below :-----van idles rough? http://howtobyme.blogspot.in/2012/01/2004-ford-freestar-van-idles-rough.html---------will not idle when cold? http://technoanswers.blogspot.in/2012/02/ford-explorer-40-will-not-idle-when.html
----------runs lean and idles rough? http://technoanswers.blogspot.in/2012/02/ford-runs-lean-and-idles-rough.html
-----------Engine stumbles coming off idle when warm? http://repairhelpcenter.blogspot.com/2012/01/engine-stumbles-coming-off-idle-when.html
------------Erratic idle on car? http://schematicsdiagram.blogspot.com/2011/12/erratic-idle-on-car.html
----------Low idle when cold out side? http://repairhelpcenter.blogspot.com/2011/12/low-idle-when-cold-out-side.html
---------Idle Air Control (IAC) Valve Replacing? http://schematicsdiagram.blogspot.com/2011/12/gmc-idle-air-control-iac-valve.html----------Engine quits at idle?

http://repairhelpcenter.blogspot.com/2011/10/engine-quits-at-idle.html

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Car overheats and Air blows hot at idle? http://howtobyme.blogspot.com/2011/11/car-overheats-and-air-blows-hot-at-idle.html
------While stop engine idles like cylinder missing? http://schematicsdiagram.blogspot.com/2012/01/while-stop-engine-idles-like-cylinder.html
---------This will help.Thanks.

Sounds like possibly more than on problem, crankshaft position sensor, or ignition module likely on starting prob which maybe affecting shifting due to hard code in ecm, or shift prob could be shift solenoid in valve body of transmission. Both parts readily available from local parts store

check ALL vacuum lines for cracks/holes and replace as nesissary

run the fault codes
check for problem ambient temp sensor, baro sensor , maf/vaf sensor problems

016 Engine Misfire Misfire Scan Data Find someone who knows what scan data is an knows how to use it .Intake manifold vacuum leak .
Rough Running When Cold GMC Yukon

crankcase sensor, located behind starter on 3.5

probably oil, it may be too thick when it's cold but once it warms up it liquefies and your engine runs smoothly. you could try changing oil, I'm guessing if you have a high performance oil the chances this is the problem may be greater since high performance things are usually geared towards working well when everything is hot

you might wanna use a thinner lighter oil