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.