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Under the carpet there is soundproofing which won't dry out this time of year without you lifting the carpets and drying it out with heat. You want to do this if its wet because VW in there wisdom also put the ECU and control systems for the car under there and surprise surprise they ain't keen on the damp conditions!
P.S remember the cartridge that holds the pollen filter is the real problem, unless this is fettled you will get water in again when it rains heavy whether the drain plug is OK or not.
You don't need to keep opening the windows to let the air out! Just run the booster fan on 1 or 2 and it will push the air right through the car and out of the vents at the back. Take out the floor mats, keep them indoors for a couple of days to dry out and if possible this weekend park the car somewhere sunny or breezy with the doors or the windows open. Always have the fan running on 1, it's amazing how many drivers still think the fan is for quick demisting jobs only; you see them peering through steamed up windows and wearing coats and hats in the car.... mostly the older drivers.
Oh and if your windows steam up easily, give them a really good clean inside. Most people don't realise that the grey film on the insides of the windows is plasticiser that has migrated out of the trim; it's the last problem the motor industry has never solved. The film attracts moisture and causes the windows to mist up much more readily than when they are clean.