That's not the engine shuddering, that's you even-gears clutch which is rooted my friend.
Don't get the car 'flashed' back to stock, you need to have the ecu wiped and then reprogrammed back to the original, FACTORY tune, not the APR version of the tune. Dealerships can find all ecu tunes now if they don't instantaneously pop up as a TD1 flag once the computer is plugged in and it is almost impossible for a tuner to hide anymore.
At an independant, budget on $1500 parts and labour, it's a pretty intensive job and takes some time. It might be cheaper than that but budget for the worst case.
Due to the common nature if these clutch packs dying, the positive is that they now only cost 650euros, 3 years ago they were 1300euros from VW when the Vw dealers here were charging $2600 from memory...
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