Mine did the same thing after changing the battery. I could barely drive it for a couple miles. It would want to die when it was in gear. Then it went away. You can tell it's still there a little around 1500 rpm.

 

Rough idling/running with no CEL is a symptom of a COP on its way out. I FINALLY had the #5 COP kick the bucket and throw a SES light. Pulled into Auto Zone, had the codes read and bought a COP. Switched it out an it fixed the problem. Also don't forget to clean the IAC ports in the elbow behind the TB, when they get clogged you will get a rough idle.

 

When you change the plugs or COP's use diaelectric grease on the COP boots(there are several threads about this).

 

I suggest changing all your COP's out after 120,000 and there so cheap now , why not? The last set I seen went for $75 new - those were factory originals. You have to watch ebay for that. dealerships and auto supply's charge 50-75 dollars for one. All eight for that on eBay.

They get weak and your truck will suffer in performance and milage.