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only thing I could think of, is that the leaf springs spread the load/weight of the car out over 2 points, and adds load to the rear frame rails, vs having it all loaded on one point with the rear frame rails/trunk floor, etc. unloaded and just hanging free.

When I did mine, it had rear suspension installed and car sitting on it's own weight (jack stands under rear end) I had to push in a little on the tail panel because I had to replace the trunk opening gutter rail at the same time, when I cut it out, the tail panel "sprung" outward, even though the replacement piece was a perfect match from AMD







I recently put two qtrs on an Ebody and after putting the rear end under the car the rear rails moved almost 3/4, I know because I took very careful measurements. The closer the car is to being "loaded" the better. I think you will find the panels will require less tweaking. (they will always require some tweaking)