The horsepower is the same at 325 and the torque numbers are only 10 ft lbs different.
The 2006 does have a newer sensor system that allows more parameters to be read by scan gage and the like.
I would choose based on color, service history, condition, etc but would probably choose the 2006.
I am concerned about the reported mileages. What were these trucks used for? Most duallys were bought to pull and unless these were RVers or horse people I would be looking at Car Fax and other reporting services. Where registered, number of owners, salvage titles, and so on.
The biggest thing is go look and drive them. Worth the flight and time if not local. Lot of hurricanes in FL during those years.