Iirc the mk4 rear side window is an encapsulated unit, meaning that the rubber is part of a sub assembly that is bonded to the glass, prior to fitment in the factory! so, the way out of this, is to fit a new peice of glass, that has the new rubber already bonded to it, may not cost that much to do, If I was you, I'd phone or talk to a local auto glass fitter, that can put you better in the picture..
Thom