Water pump/thermostat parts are about $630. And around $600-700 for labour as its not a fun job. Water Pump & Thermostat Housing Bundle (MQB) EA888 Gen 3 - 2.0 TFSI EA888.3 – VAGPARTS Australia
Best off to stick to VW genuine parts for the water pump as they have revised it a few times to try and make it better. Hopefully an aftermarket company will make a cast aluminium version soon - but none are available yet.
The high pressure fuel pump which is bolted to the head of the engine (and is run off the inlet camshaft) is $580. You could easily replace this yourself with some basic tools if you are mechanically minded. Otherwise I cant imaging you would be charged more that 1hr labour ($150 ish) to replace it - its a pretty simple and quick task. 06J127025L - High Pressure Fuel Pump - Audi & Volkswagen 2.0 EA888 – VAGPARTS Australia
One thing to check with the fuel pump, are you sure its not just a perished o-ring that is causing the leak? Is it leaking oil or fuel?WHT005184 - O-Ring for Fuel Pump EA113 – VAGPARTS Australia
So $3,100 does sound a bit rich. I would think $2,000-2,200 would be a more realistic price for both items to be replaced.
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