Here are my prices on an SQ5, same 3.0T motor though.
Water pump $877 - $640 labor $237 parts
Thermostat - normally $1150 since it under the supercharger, I was having the PCV shutoff valve N548 replaced so they had to remove the supercharger already. reduced labor thermostat price $478 - $400 labor $78 parts
Good idea having the intake valves cleaned, I forgot to even ask them to inspect that. I'd like to think if it was extremely bad they would have mentioned it, but who knows, mine is 2 years newer than yours and this work was done 2 years ago.
Also maybe replace the serpentine belt while they are at it if you have not already had that done.
Looks like they might be giving you a better rate on the thermostat and water pump since you are having the valve cleaning. If they'd still honor the other prices without the valve cleaning I'd say it was a bargain.
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