I recently purchased a '94 FD and after removing the '99 Spec wing I noticed there is a large gap between the hatch and the tail lights ('99 Spec). If I line up the hatch so it's lined up with the corner of the quarters there is ~1/2" gap between the hatch and the tail lights. If I adjust the hatch so there is an even gap on the sides and where it meets the roof, the passenger side is close to the tail lights. It's almost like the hatch needs to pivot. Stock hatch from what I can tell.

I'll try to post a picture but any advice is appreciated in the mean time.

 

I should also say that the tail lights are flush with the body and with each other so I don't think that they are the issue.

 

Have you ever gotten a car fax on the car to see if it was in a accident? If it has the window frame could be bent.

You could also take the whole hatch glass off and see if there is something in the alignment holes blocking you from getting everything lined up.