Dad's 06 megacab has the 5.9 with an auto and he pulls 23-24mpg all the time. Granted 80% of the driving he does is two lane highway at 65 mph.
If you buy a 6.7 and delete the DPF and the egr you will void the warranty and fail vehicle inspections. Of course the inspections is only a problem if you live some place that does it.
The auto is fine at stock to a little above stock power levels. Its the 21 century the mileage difference between the auto and the manual is probably not even noticeable. Especially depending on the gear in the axle. If the manual has 4.10 and the auto has 3.55 guess what the auto will get better mileage.
My main advice would be test drive a couple and pick the one you like driving the most. If you live in a big city do you really want to row your truck in stop and go traffic every day?
1998 3500 4x4 5 speed reg cab dually 12valve
TST #10, ATS exhaust man, 5" turbo back exhaust twin 5" stacks, SB 13.5 clutch, BHAF, DDP 75 hp injectors, 3000gsk, timing set at 16