I couldn't really find any options for my mk3 either... it seems your best bet might be to refurb what you have? I just got some double sided sticky automotive gorilla tape stuff so that I can make sure the one on mine that is loose doesn't fall off...
If its completely missing, I haven't really found a good resource for this... I've contemplated filling mine in for a more "modern" look, but I'm not particularly proficient with bodywork. My understanding though is with how deep you'd need to fill it, any kind of body filler that you'd use would wind up cracking because of how thick you'd have to lay it on. Maybe you could figure out how to weld in a patch along the side? I'm not sure how that would work with the thin sheet metal of the door panels, and potentially stuff behind it... >_>
