I did a bunch of things to my 2003 6.0, some good and some bad. I used elelbrock shorty headers with titec coating, they make it sound and run better but lasted 5 years. The flowmaster catback sounds great in the single exhaust style but only lasted 3 years and was a rotted mess. I have a hypertech programmer that works well with tire size changes, shift points, slight power upgrade etc. The aem brute force that was suggested is the best one since its a dry element. Also have a jet performance throttlebody spacer , bbk throttlebody, msd wires and bosch plugs. Seems to run real well with 37s and 4:10 gears.
Ill be stepping up to bbk stainless headers and a stainless magnaflow catback, which with living in the rust belt what i should have done years ago. Also just got off the phone and will be ordering instead jba headers and stainless dual exhaust.