To close this out:
Skoda came good on paying for all the repairs, including the water pump.
Whilst the car was off the road for two weeks, I got the shocks replaced (4xOEM) for ~$980 inc GST.
Brooks Skoda did a fantastic job, and ended up giving me the loan car at nil cost.
The car runs like new now. The day after collecting it we took it on a 1 week, 1000+km family holiday. The DSG is very smooth, as are the new shocks.
Once I wash her and get a decent photo, I'll put a thankyou post on Skoda Australia and Skoda AU Facebook pages.
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