OEM bumper and lights? I had that issue with the tail light not being flush because of the crash beam when I went to a JDM rear. Not sure if that's your issue in this case but I had to cut the sides back some more to get it to fit OEM.

 

OEM JDM rear and OEM JDM evo 8 MR tails.

 

definitely file for diminished value and bring up the issue with the gap to the body shop. I had a similar experience with the body shop i took my s2000 to when i got hit. Its a professional shop and my cousin owns it but he still tried screwing me over in the end with not fixing the little issues.