I have an 02 F250 super duty. I bought it new.
I have a K&N air cleaner, 4" down tube and exhaust, Hi flow muffler and a superchips tuner.
The truck worked well for years with my modifications. The last couple of years, though, i have had problems.
With the truck programmed to any of the settings (other than stock), if i drive it hard, or pull a big load up a hill, the engine light comes on.
For an experiment, i programmed it back to stock and took my travel trailer on a trip. Clearly the truck was not able to pull any load up a hill. The engine looses power and shifts down to second. Once in second it continuously cycles - the RPM goes up a bit, then the waste gate opens and dumps pressure, then the RPM goes back down. Over and over it cycles. I have to back way off the throttle, eventually it shifts to third gear and stops cycling. But not much power
With the truck programmed it has plenty of power. It is possible to pull almost any hill without the check engine light coming on as long as i am careful to not push it too hard.

My thoughts have been to replace the turbo and wastegate.