From what little I know about turbos, I think the turbo is your problem, not your fuel. Or maybe they are linked. But you said already the turbo overboosted, and still is above 2000rpm. So why is it, wastegate stuck shut or what. Does the fuel injection get boost reference, so when the turbo spiked it added fuel as well.
I mean I know you guys turn your fuel up to get a little more out of the truck, but what or how does that link to your turbo boost. Just a thought I guess, but I am leaning toward a boost leak in a reference line to maybe he wastegate. I havent dug into the deuce turbos, so I am not sure how they work. My 2 cents is its somethin with the turbo. Maybe you thought your old motor was gutless because the turbo was leaking etc, and something broke loose as a coincidence with your new motor install.
I would at least see how long the motor last at 40psi so that we have something to go off when we play with our trucks.