I can tell you that it is a fact that diesel is more expensive per gallon (duh!) but it is cheaper to run a diesel truck per mile over a gas truck. As for mileage, it seems that you will get better mileage from a 98-02 model truck.
03-04.5 will be your best bet as far as mileage goes. Mileage is a little better with a manual, but if your towing, I would recommend an auto. The 48RE is a good tranny, as long as you take care of it. A stock 48RE can handle about 70 hp over stock before you start having problems with it, mainly converter slippage. It is entirely up to you what you want. Good LuckWhat years of the 3rd generation 5.9 would be okay? Any significant changes? What about auto/manual? I heard the autos are the weak point, and the manuals can take more of a beating.