Booked into Wishaw Volkswagen (Central Scotland) to attempt and try my luck with my new daily 2005 TDI. Surprisingly the only rust on the car is at the front on the common spots for the Golf MK5 such as the wing and the sill below the wing. It may be over before it started, but before spending money on a rust repair I'm wanting to see if Volkswagen can honour their warranty with such a rusty MK5.
Here's some images of the rust in question (Crappy iPhone Pictures):
Driverside:Passenger Side:If Volkswagen decide to decline which I've got a high feeling they will probably will I'll end up getting new wings painted with the foam trimmed or removed, properly clean the wheel arches effected and attempt to lower the effect of the rust and hopefully get it properly repaired.
I guess the only way in the future to stop the sill rust is to properly clean behind the sills every couple of months or once a year to stop the build up of dirt and leaves. I'll post again after speaking with Volkswagen to see if they can honour their warranty.