Rough idle on cold start up
 

I have the rough idle too, usually only when I start it first time in the morning.As for the whining noise, do you still have your cross bars on top? That does tend to make a whining noise

I have a 2001 Jetta 1.8Turbo that was doing the same thing on startup. Took it to the dealer and they said it needed a update on the cold starup software to the computer. It seems to be doing fine now.