I've seen problems with tuning cause this, as well as bad turbos. My recommendation would be to try different tuning first because its cheaper than a new turbo. The H&S can cause a lot of problems and may not allow positioner codes to set. I have a 2013 in the shop right now that is doing the almost exact same thing you are talking about. H&S tuner.
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'85 Yota Crawler-2l diesel, custom built VE (by me), custom T25 turbo. Slow but fun!
'95 Cummins grampa truck, embarrassingly stock
'12 Cummins, deleted
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