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.

 

First, let me welcome you to the Oregon Chapter. I only have IDI Ford diesels, so I'm not much help..............I would contact FN74 ( he is one of our sponsers) He has a shop that specializes in PowerStrokes, and SuperDutys. He is located in St Helens Or. Linky: StrokeShop - Home

I myself would not suspect the turbo or waste gate. If either one of them was bad it wouldn't work OK with the tuner.

 

Post this in the 99-03 7.3L forum of FTE. There are lots of folks there that know these engines (and tuners) well! They will pitch in and help.