Now you know why it was for sale...
Seriously though, this happened to me with a twin cam Corolla. I only found out when someone rear ended me and the panel beater showed me what was lurking under the trim. I should have been suspicious when the parcel shelf didn't fit properly.
The issue may not be the tailgate itself but the rest of the car. ie the tailgate is actually straight, but the car is bent/twisted so the tailgate won't fit properly. That could be why you've been quoted $6K.
MY12 VW Golf 90TSI DSG, MDI, Towbar
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