One thing I've just thought of . . .
I have a power commander on my NA stock Gen 1, I had it dyno tuned and a map made for my PC3 by the tuner.
It went fine, and then a year later I fitted some new stage 1 Yoshi grind camshafts.
Then it had a hesitation, a 'miss' like the engine cutting out momentarily as I put it in 1st and released the clutch to move off.
This happened frequently, almost every time I released the clutch in 1st with revs just above idle.
I disconnected the PC3 to see if the fuel map in it was out of tune for the new cam timing and sure enough . . that was the issue.
It never hesitated or mis-fired again as I took off slowly in 1st.
I'm not suggesting you unplug your Power Commander, your turbo set up is going to be tuned by it, BUT I am saying maybe it's not correctly fueling at the point where it 'cuts out' as you put it.
Just something to chew over really.
I hope this is helpful.