sounds like the rails are still buckled in somewhere? Is there a visible point of compression in the rails? The tail light panel attaches to the rear lip of the trunk floor, it's possible you could replace the trunk pan and have the quarters and trunk all line up but have the rear crossmember in far enough where you would have to shim the bumper to get the correct gap if the rails are still pushed in somewhere.

One last question, is the car driveable? I'd be curious to know if it tracks straight.