Early 06 MPG Issues

New to the site guys, looking for some help. My dad 06 mega cab cummins is only gettin 13 mpg city and 17 highway. Truck has Afe stage 2, Edge with Att. Magnaflow 5in exhast. 31,xxx miles. Trying to figure out what might be the issue. I just recently changed the fuel filter and cleand the air filter. My dad seems to think the is a different computer program between the early and later (600/610) trucks. Wondering if there is any truth to this? I figured this would be the place to ask the question.
Thanks guys
Mike