'USED to have a stage 2 tune' and 'It still has the deletes, but is stock'
If you are on a stock tune, you need tuned. TGV deletes are beyond a normal 'stage 2' level....what else is still in there? Does it have an intake? a downpipe?
First, you need to go over the car and see what is currently installed. Then you need to flash to a tune that supports those parts.
edit: Additionally, TGV deletes are normally not done till you are at least planning on a larger turbo and injectors.....do you know if those were changed and still in the car?