Thanks dipstick,
I took the car to the dealer and they seem to think it needs new door seals. They have ordered them and are being fitted on Wednesday. I'm not sure, I think it comes from the windscreen. I pressed it hard in the top corner and most of the noise stopped so I think you are right about the seal. I'll let the dealer replace the seals and if that doesn't do it I'll mention the windscreen seal. I still have 2.5 month of warranty so hopefully it will be fixed by then!
I have adjusted the sunroof, it's still a bit low on one side but it's at the end of the adjustment. I may have to pack it out a bit.
I to have a CD from ebay. It has a few things on the MKII, wiring diagrams etc. but not too useful. Has anybody subscribed to ALLDATA?