[FTF Automotive]

Gotta remember that just because they have a machine that is laser aligning parts, which parts is it measuring and aligning? If the exterior of the body is now square, that doesn't mean that the structure that is mounted to the body is square. I would get underneath it and check to see that they didn't accidentally overpull the frame rails to one side. Looks interesting, could be many things.

 

[FTF Automotive]

At this point, as previously stated, you are going to have to take out some variables. You know for sure, that you have differences in mount design side to side. Fix that. Without it, you are pissing in the wind. It is hard to diagnose any problem when you have 50 other things all wrong. Get the correct designed parts needed, whether they be original style or aftermarket. You can tell very easily if the rear end is sitting crooked if you measure from front of wheel to quarter panel on both sides as someone else suggested. That will show you some of your problem. I would try to get a mini square and place it on the frame rails in various places and see if they are square to the trunk pan. This is not going to be a great test, (other panels I.E. the trunk pan, you are assuming are square) but if there are big gaps, it could show you if the frame rails are really off. Then start taking measurements from outside of frame rail to trunk drop offs on both sides. You really just need to start measuring everything you possibly can from side to side. Measure and mark center line of the car on the gas tank, and measure each rail to the point. If the frame rails are shoved over, that would explain the axle problem.