When I start my truck for the first start of the day it runs rough and feels like it is missing. It actually shakes while idling.It will do this for a few minutes until it starts to warm up then it runs fine. My buddy has the same truck and his doesn't do this. Both trucks are completely stock.
Stiction or faulty glow plugs. Any codes?
You can throw a 16oz bottle of Archoil in the engine next oil change, if it's stiction it should clear up. Lots of guys swear by it and many call it snake oil and say pull the injectors and sand the spools. Pick your poison. At least if the Archoil (or Rev-X) clears it up you'll know what it is. FWIW both Archoil and Rev-X have kept plenty of trucks from early injector work. (Hot Shot's Secret may work too, I have no experience to say)