It'll cost less to delete an early 6.7 than buy an exhaust brake for a 5.9.
I'd buy a 6.7 for the 6 speed auto but if going manual then a 5.9 would be preferable.
Overall, I'd shy away from early 6.7 Rams if you are opposed to deleting it down the road if you have recurring emissions problems. Seems 07.5-08 had more emissions issues than 09 up, they got it dialed in better just like the other mfg after a couple years under their belt.
Early 4th gen Rams are the same chassis and drivetrain as 3rd gen 6.7s with much improved cab/interior/amenities and with Rams new chassis and emissions in '14, they seem to he about the same price as late 3rd gens. I'd go for a '10-11 model if going used pre def Ram.
Hope they get your soon to be ex truck sorted out tomorrow........and economically!