The 6 cyl cars should have 4 lugs and the 8 cyl cars should have 5. Sounds like someone swapped in the 302 and atleast got that part straight. They would have had to replace the rear axle to get the 5 lug, so not really a surprise to see a 9" back there.
Another possibility is that the car was originally a 302 and someone swapped the VIN. Have you checked all the VIN locations to be sure they match up?
As for value it's a personal thing. If the car originally came with a 6 then it's obviously not original, and would be hard to take back to original so for some that would decrease the value. However many would consider a 302 an upgrade from the original 200 6 cyl so they might think it's worth more. However, if the swap was done poorly it would definitely decrease the value.
If you want to car to show and completely restore then the engine swap is a problem. If you want the car to drive and have fun with, then it's probably not as big of a deal.
Personally I think the resale value of a GT/CS does suffer with this type of major change. People shopping for a GT/CS will typically be more interested in originality then those shopping for a standard Mustang.