A common problem with the Mk3 convertible is the door shut line. The problem being that it pushes out at the bottom once the door seal is fitted causing an unsightly door line. This is because, unlike the Coupe, it has no where for the glass/frame to push against at the top of the door to lever it back.
The fix for this is simple (passed on to me by Charlie Dodd), although a little unorthodox.
First you need to undo all the fixings on the door to the door frame. ie Rivets/bolts etc so that the frame is loose in the frame. Next you need to get a second hand to twist the door in at the bottom, whilst out at the top, so that it is actually over twisted to the position it will eventually sit in the door aperture. Whilst the door is in this position, you redrill new holes and refix the frame to the door. When the door closes it 'should' be a lot nicer. The theory is sound so should be fine now.
Recheck your hinge positions for door height and adjust accordingly (if necessary).
Happy to discuss
Cheers,
David