I've owned a 2002 Cabrio GLX for the last 4 years and I've became best friends with my mechanic.

Yesterday I got similar issues that you've described:
1) When I left my car in the garage overnight I noticed all the windows were open.
2) The courtesy light on the drivers door wasn't working.
3) When I was driving, the alarm horn would sound 3 times.
4) The vanity lights were not working.
5) The factory radio kept going into SAFE mode each time I shut off the engine.
6) When I opened the driver side door the windows would go down.
7) A 20 Amp fuse towards the far right of the of the fuse box was blown.

So today I took it to a trusted mechanic as I haven't had much luck with the local VW Dealer. The mechanic replace the 20Amp fuse and as soon as the vanity light was turned on, it blew again.

So he took the drivers side door panel off and found that wires coming from the door lock had been rubbing against bare metal of the door and had burnt out the insulation and were making contact. He rewired that section, 6 wires in total and put the door panel back on and everything is working as it should.

Total cost of repair was $200.

I would suggest you ask you VW dealer to check the wiring in the drivers side door first and also refuse to pay for all the components that they've changed ($2K bill) as they haven't fixed you issues. Write to corporate if they refuse.

Hopefully your problem with be fixed and your daughter can enjoy the car.

Its a great car when its working.