SO, I bought a 93 FD with no tail lights, and before test fitting a pair of tailights, I sent it off to get repainted and such.
Well, The right tail light does not fit correctly. It overlaps about a 1/8 of an inch over the rear quarter panel. All the doors/hatch line up fine and such. Im thinking maybe the rear quarter is miss aligned? Could it be anything else? Anyone have this issue before with rear quarter alignment?

(Clean title car, hit in the front once before I think because the radiator support was a little crinkled)

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It's almost always a sign of a previous accident repair of the rear quarter on that side. I would show the body shop that did the work. It may need to be re worked. I had a similar issue when repainting my rear bumper and my tail lights say up too high on the passenger side. The metal needed some massaging and we were able to get it to fit correctly. In my case the taillight say too low
Compared to the center light. They had even tried stacking washers under it. I had the bodywork done by a pro and he got the fitment spot on.
The tail lights fit perfect now but the bumper to rear quarter needs some work still to ft OEM. It shouldn't need any body work. Just some adjustment. The rear bumper has some adjustment where you can move it up and down a bit.
If you look at my build thread you can see what I mean.