Ok from the start. Bought the truck and got it home. Had a built engine in it with a 48re and wanted to put in something lighter, since the truck is a mega cab, to make it a weekend track warrior. Truck was originally a manual g56 then got a 48re. Pulled that engine got it in the blue truck in my picture. Used the ECM from the blue truck and got her up and running in front of the 68rfe for the time being.
After a bit and once I got the engine from my blue truck back to stock. I pulled the 68 with the engine/Trans/front clip harness. Put the engine and harnesses from the blue truck into the mega cab with the ECM originally from that truck. Swapped the columns and manual transfer from my blue truck as well. Mega cab originally had an electric transfer. So at that time they had swapped keys as well. Got it all together and tried to load a tune before trying to start. Got the error 0549. Tuner said to give it a try starting so tried and nothing. Just cranking and the clicking/pulsing of the airdog. At that time we tried swapping ecms between trucks to see what happened and got the same thing. Swapped them back to the trucks they were originally in and then swapped the columns back as well. Just swapped the shifters this time. So the correct key it back in the correct truck. Still nothing so I swapped the dashes to rule out those harnesses not meshing with the front clip/engine harness and still the same.
That's about as broke down as I can get the whole ordeal. Only thing that makes sense to me like others have said is when I turned the key the first time with the wrong one in there the ECM was like whoa! That ain't right and locked out. Sometime this week I'll get her on a roll back and see if the dealer can flash it and check the key making sure it's linked back up. If I don't figure it out before then. Also I really Appreciate all the input guys.