[TacSat1]

What 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.

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 Luck