Really hard to tell if I do not no what you have checked...could be a loose or cracked hose, software issue (probably unlikely), etc...I would check the turbo install since that is where the problem started, check all the hoses, etc
My guess is something was damaged or knocked off during the turbo swap and it is causing the turbo issues...it only takes one crack in a hose to cause problems. Check all the vacuum hoses under the plastic cover near the oil cap...make sure everything is connected right...also check the intake pipe, they can crack and you would not even see it especially if you have taken it off, they get really brittle because they are plastic, also was the turbo a rebuild or did it come from China...you could have a bad turbocharger and it may not be spinning correctly, that will cause the turbo to produce odd and random level of pressure...
