I replaced the PCV with the newer version so now the seal for the PCV near the turbo inlet is brand new. I also removed and reinstalled and tightened up the turbo inlet seal and jubilee clip.
I think I'm making progress, but it's hard to tell if it's just because it's more eager than before, so it's moving passed the vibration rev range quickly as it revs up faster, or whether the combustion process is better. I know sometimes adaptations take awhile after a change. Either way it's an improvement.
Having said that, it did another regen today and it was smoother still.