A vf52 is not even close to the same turbo as a vf40/46 It requires a custom tune! You cant just use an off the shelf cobb stage 2 tune! Also the vf52 uses a different restrictor pill size if it didnt come with one.
If what I am reading is correct you should have done more research before installing that turbo. Dont go into boost at all, get the proper size pill if you dont have it, and get it pro-tuned ASAP!!!
Just re-read it and you did injectors too, those also need a custom tune.....no wonder your car doesnt run right....I'm surprised you can even drive it...get it pro-tuned by a local reputable tuner ASAP!!