3rd Gen. Hemi Swap Questions...
You will want to use a 2004 or newer truck engine ECM. It has more tunability than the 03. You will need to have a Diablo tuner for what ever the engine/ECM came from as well as you will likely need a Diablo dealer to write you a customized tune (CMR tune) to eliminate some of the items not needed and to adjust some of the things needed to match up with your vehicle.
We are about to start dealing with those same issues on our shop projects.