Check for frame damage. in the back trunk an the front. alot of times VW owners will just slap on a new front or rear bumper an you would not be able to see the damage at first glance. VW's are basicly aligned right from the start little to adjust so a bent frame could mean going though sets of tires like mad.
Also check to see how smothly the trans shifts. any clicking or slight grind when changing gears could mean the trans is on the way out VR6 trans are very expensive an hard to come by used
As for the motor if it's smoth an no blue smoke you should be good. if there is a slight hesitation it may be due to faulty wires. Most people will not change the wires on these cars because of the high cost of doing so. ( not that high though) it may be in favor to you as a price hagling tool.

New wires an sparkies new car.

there are some other issues such can be found on edmunds.com Where owners shed there headaches . Not much though with this car