Changing the transmission fluid is considerably more involved than changing the engine oil because you do need a few special tools.
First, you'd need a service manual from Bentley publishers, either CD-ROM or a web-based subscription.
Bentley Publishers - VW
Second, you'd need a VAG-COM diagnostic tool from Ross-Tech so that you could properly monitor the fluid temperature.
Third, you'd need 4 very good quality jack stands and a level work surface as you have to raise the car enough to work under it while it's running. Seriously.
Fourth, you'd need the fill tool which hangs from the hood and feeds the fluid through a tube with a special shaped nozzle that fits into the drain plug opening. I've seen them online before.
You get the idea ... not tough, just very procedure oriented.
But, in your case, since you are already having transmission issues, I think it would be wise to let a VW dealer perform any work so that you protect your warranty.
I really do believe this has a good chance at solving your problem. I am dismayed at how mechanics have become part swappers all driven by fault codes.
Like I said before, good luck getting past this annoying issue ..
PS - I already most of the above tools so it's easy for me to sit here and be an armchair mechanic.
Modified by pretendcto at 6:53 PM 10-18-2006