It seems hard to believe that there is something that horribly wrong if the noise goes away once it warms up. HEMIs are pretty reliable I think, though they are known for dropping valves in that generation of engine. However, this isn’t a noise that I could imagine would get better when the engine warms up, much less completely go away. It would be useful to know what malfunction codes are stored as well. Can you get them read and post them? You may be able to try the “key trick” to get the codes–without starting the truck, turn the ignition on-off-on-off-on quickly and leave it on. The codes will be displayed on the odometer or dash display or blink out on the check engine light. This has worked with Chrysler vehicles since the early 90s.
One thing about the Chrysler MDS system is that it’s very important to use the correct weight of oil, as the system is oil-operated. I think your vehicle calls for 5W-20 oil. If you have been using anything heavier, especially if it’s getting cold where you live, this can cause problems. What does the oil cap say, and what have you been using? If you’ve been using the wrong weight of oil, change it immediately and see if it helps. The dealer or shop could easily have put the wrong oil in it too. Mine likes Amsoil synthetic 5W-20 very well.
I agree with NYBo–you may need a new shop.