it needs a complete pcv job or you'll be doing the cam seals too.

the engine needs healthy vacuum to run properly.
now it runs with positive pressure , but not well.

Try not to engage the turbo until you get that PCV taken care of. I feel like that sputter could be related to a dirty intake, but I'm still a novice in these things. Refresh your fuel injectors when you have the rail off during PCV service. It's not unlikely doing a real nice combover during intake...