A cold engine can amplify some symptoms. I would think you'd still be grtting some symptoms after the truck is warm, just not as noticable.

Have you had the codes pulled? That's really where we should have started. That would show us if the problem is in the IAC, or possibly the EGR if the injectors turn out to not be the culprit.

Here's another possibilty, strange as it sounds: Check the fan for cracks or breaks that could throw it out of balance. Those plastic fans are notorious for cracking. The fact that it causes a problem only when cold would be related to the fan clutch.