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Is there a way to get the trunk lid to set lower into the cavity, shims somehwere perhaps?
There was a ton of bondo on the filler panel perhaps that needs to be pushed up.
If I'm viewing your photo correctly and it looks like the deck lid is higher toward the rear glass opening. You would place the appropriate shim under the deck lid hinge bolt closest to the rear of the automobile on the side that is high. That will force the end of the deck lid closest to the rear window opening down. When doing this be certain to loosen both hinge bolts, insert the shim and then tighten both bolts once alighment is complete. This is better accomplished with 4 hands.
With a shim the appropriate thickenss this should give you want you want.