Exhaust leak, odd whine sound and misfires... kerma tdi problems...

never had any problems out of my car until I had a boost leak that destroyed my vnt15, I put a borg warrner s7 v2 turbo on along with a tune a 3 bar map sensor new vnt actuator new egr/asv all from kerma cleaned and inspected intercooler pipes with the exception of the top one.
It was taken off first and was somewhere in the Jetta covered by other parts and I forgot about it. Well it was the one with the boost leak.
After I got everything on I took the car on a test drive to find I still had low boost. Drove it a 2nd time before finding out where the leak was. got
It fixed and everything seemed to be ok except the car would misfire when cold if you give it throttle past halfway.
Did not do it every time but only did this when cold or halfway warmed up. It would loose all power start running rough and a little bit of white smoke.
If I let off the throttle it would go away and I could resume on my way.
So about 1500 miles on it I upgraded to a fmic and noticed that there is exhaust soot on top of my vnt actuator on the turbo.
Kerma tells me I probably put an gasket on backwards... I did not believe him but I ordered a new gasket set and pulled the turbo.
Well it was not a gasket problem it was coming from the vnt actuator arm that goes through the exhaust side of the turbo to actuate the vines on the turbo.
So sent the turbo back to kerma. They sent it to a 3rd party inspector and they took apart the turbo cleaned and tested it.
They said everything is fine and finally got it back to me almost a month later... would have been even longer if I would not have been calling them to speed up this process. I needed the car for a road trip.
So got the turbo back and now it makes this odd sound that starts about 8psi it sounds like a supercharger whine or the feedback sound you get when you are playing music on a iPhone in your car and hook it up to charge...
But I needed the car for a trip and I took it. It drove fine on the trip got good gas millage. But 1500 miles of mainly highway driving and the exhaust leak is coming back... kerma is saying they will not take care of me on the exhaust leak because the boost leak when I put the turbo back on compromised the turbo... they said they will try to help find a solution that is cheap but so far have not come through and will not respond to me anymore. The leak is not as big of a deal to me as this horrible noise I am now getting after getting the turbo back from them. I did another boost leak test and I don't have any and was not able to recreate that noise by pressurizing up the system... so that tells me it is the turbo that is making the noise. What could it be and is it going to blow up on me?
Also the misfire seems to be getting a little worse.
Have had it happen a few times since the turbo went back on and it got so bad the engine actually shut down... I am at a loss never had this misfire before the tune and new turbo... autoscan show nothing but a missing asv because I want back to the test pipe while I build a stealth race pipe.
I am to the point I may even buy a different turbo or even a used turbo to see if some of my problems go away...

So, you got all those parts and didnt fix the boost leak first?

What might happened was that the turbo over-spooled due to the boost leak because the ECU kept asking for the requested boost and it didn't meet, so it opened(close, not sure) the vanes till the turbo went into over-speed and the bearings are likely damaged..

Now, if the turbo was reviewed by a 3rd party after that and they didn't notice shaft play, that is a bit strange.

The part of the car shutting down, that smells more of a lack of diesel, clogged fuel filter, bad injectors, can be a lot of things, are you running the original injectors in your car, they are a bit small for such a big turbo.