First off, how much is the right rear corner off from the left?
I'd have them put it up on a frame machine and see if it's off by the factory specs. There are a lot of times when there's just enough damage for things to be off without it being visible to the naked eye. Also, check the gaps all the way around the rig. Everywhere that a moveable panel or bolted/screwed on part meets and should be in a straight line. If anything doesn't quite line up, then you might have a frame issue.
If you don't get anything there, then start looking at the rear axle. Everywhere there's a connection to the vehicle should be suspect. Control arm brackets, spring perch, trackbar and shock mounts, etc., etc.
If you don't find anything there, the last place I can think of to check would be tub mounts.
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yeah, it is another red wrangler....