On my 08, the ECM was bolted to the side of the engine. Is your 06 the same way?
If so, did you keep the ECM from your original engine, or did the new engine come with a new ECM?
To me it sounds like an immobilizer issue. I think Dodge calls it Sentry Key or some such thing. Anyway, there's a chip in the key that has to get programmed into the BIU/ECM or the truck won't start.
Might be time to drag it to the local dealer.