i ordered late 68 full rear quarter panels, the place where the side scoops go, are different from what is on my 68 gt/cs. the rear quarters that i got, look like 67 rear quarters that haven't had the openings cut out. the contour of the indent differs between the two. has anyone ran into this problem?
The difference between a late and early 68 quarters is only the rear area for the side markers. The late one (from 15/02/68 onward) have no marker indentend area, because marker were mounted flush. The early one have a dished in recess to mount the marker bezel flush. There should not be difference in the front scoop area.
Keep in mind the GT/CS were made on the same assembly line as the regular Mustang and made during a period where both cars could be made, so the car shell/body was identical, and the GT CS specifics parts were added when the car was a GT/CS.
As far as the 67, they're identical with the late 68 except for the cut-outs for the 2 simulated side scoop on each side.
I know that because on a previous restoration of a 68 Mustang, I wasn't able to find NOS 68 quarter, but I found a 67 one, so I bought it, and I used my existing quarter scoop area ( I cut it out off the 68 I was replacing, since this area was intact) to mount in a similar cut-out I did on the 67 one so it "became" a 68 Quarter. I wanted NOS quarter because of the better fit compared to repro ones, at least that was problem 15 years ago.
In your case, it may be a problem of Quarter die accuracy? Who manufactured this new quarter? Can you post a picture of the area to see this difference?