I had a 1.8T petrol Passat and one of the things you should very definitely check is the electronic control unit for the central locking and alarm system. The unit lies on the floor at the passengers side and water gets in under the carpet and corrodes wires, terminals, the unit itself, everything and you're looking at over a grand to sort it all out.
First inkling I got was when the door courtesy lights stopped working then the central locking started acting up. One day the car locked itself with the key in the ignition when I was outside it. I only got the one key so had to call a breakdown truck who managed to get in so I hot tailed it down to Timpsons and got a spare key cut for £25 (never did get it programmed) but at least I had a key that would open the door.
The water comes from the bulkhead scuttle area at the bottom of the windscreen, either rain falling or washing the car etc. There are two plastic drain tubes, one either side, which are supposed to drain it away but they inevitably get blocked up. I couldn't get mine to clear so had to drill two holes to let the water drain away - and make 'em big ones, the first ones I drilled were about 3/16ths but they choked up so I had to make them about 1/2".