Are you logging boost level when it is sputtering and missing? It sounds like maybe you are just boosting really high momentarily then fuel pressure drops causing sputtering, missing, KR.
Don't ask me why but I can get boost where I want it and think I'm making good progress with my tune then out of nowhere boost will be lower and or higher in places than I had it...It has more to do with the commanded torque I think....The boost is an arbitrary thing, the car is attempting to give you the torque you are commanding and the boost is what it is. It's weird and I'm still learning it but my point is that boost spikes can happen inadvertently and when fuel pressure is low the door is open for sporadic behavior.
I wish you could log in livelink gen 2. I'd send you the config file with what I log and I'd love to take a look at some of your WOT pulls.
Did you say that it happens right after you floor it at a downshift for wot? Boost could be spiking pretty good there....I've had high boost tip ins with multiple tunes including tunes that I paid for.