First off...how could you have let mice find the time to build a nest in your intake???
Treat your VW with some love....drive her daily!
As for the leakage, a similar situation happened to one of my buddies A6's. His car had a line that was leakin from the ac duct and was soaking his floor in the back right seat. So if this sounds familiar, bring your car to the dealer and have them check the ac lines or something. Once the leak is taken care of...the mildew will eventually clear and you can fumegate your car.