Welcome to FTE. What are you using to pull the codes? The free scans at the parts stores won't read the engine codes in these trucks. Can you describe the rough running a little better? Does it feel like a miss, or like the engine is not firing on all cylinders?
If the CEL (check engine light) comes on, there is a code there. You just need the right kind of code reader to see it. This kind of sounds like a loose UVCH (under valve cover harness) issue. When things heat up, the connection gets worse. If you have an ohm meter handy, read through this thread that has pictures and the test procedure so you understand what you're looking for. http://www.ford-trucks.com/forums/80...ck-shakes.html
I have a 99 F350, 7.3 that after warm up the service engine light comes on and truck runs very rough. No codes will come up. It runs fine until warm up.
The truck has 245000 miles on it with no real problems. The cam position sensor has been changed under recall, and of course the high pressure pump hose o-rings.
thanks in advance,
I agree with Chris.. It sounds like the famous under the valve cover 9 pin plastic piece of junk connector is loose... You can remove the cover/s and made a shim out of a 25 cent coin to keep it tight... You can reuse the covers gaskets, so the total cost for both sides is 50 cents (plus your labor)... Yes, if you have CEL light than you have a fault code recorded.. probably a P1316.. Also, check the wiring under the covers for rubbing.. Another area is on top of the driver's side cover. The main wire harness rubs on the top of the cover.. Let us know what you find..