I had an Acadian Blue coupe and they usually came with the two tone blue interior. It is not a bad combination but not on the top of the disirability list. Your questions is about the value on your car in its original color versus the value of your car in its current color. IMO since the Bullit look IS popular, that the color change went in the right direction. It also could have been painted black and perhaps increased its value even more. (since it is my opinion that black Mustang GT fastbacks are on the top of the color vs value chart) Since the Moss Green over black is a more desirable combo than the light blue I feel that the value would actually be the same or slightly higher for the car like yours. As an original Acadian Blue it would have had a certain value based on originality and matching door tag data that would appeal to certain groups of buyers, but would have turned off a block of Mustang buyers that would have passed on an acadian blue car. However, Mustangs are unique in that they paint their underhood area black, making a color chage much easier to do and make look correct. So, in the dark green over black the car should appeal to more potential buyers that would be willing to overlook the color change/door tag issue, especially if the paint was done correctly without overspray all over everything. I think that overall your car might be worth slightly more in its color changed condition than in the original color.
Just my nickels worth
I don't know a lot about anything, but I know a little about everything.
Built a 1967 Shelby GT-350 Convertible Replica, a 67 Vert resto-mod and also built a 427 FE 67 Shelby GT-500R (R Stands for Replica). 427 Side Oiler, toploader 4spd, 4 wheel discs, 9" traction loc and a perfect body. What more could you ask for? Now I car hunt and horse trade and I am currently looking for the next project! Always seeking that elusive "reasonable" Shelby.