Based on the other things in the photo that we suspect we know the color of, and how black-and-white film reproduces such photos, my guess is the car is blue. Red tends to look much more grey in a B&W pix.
However, since there were green cars, as noted by Jim P., there's a possibility it could also be a metallic green. Similar appearance in B&W as a metallic darkish blue.
What color was the 1963 Michigan license plate? That might help.
Just my $0.02 as a long-time car photog.
The Registry indicates that CSX2048 was repainted a custom “pearl” paint and used as a show car.
Based on the Registry colors other than red, black, and white started early in the second chassis contract.
CSX2104 finished in AC Cars “Bright Blue”
CSX2108 finished in AC Cars “Princess Blue”
CSX2112 finished in AC Cars “Vineyard Green” and beige interior.
Bright Blue was similar to Ford Guardsman Blue but definitely not the same (I have an original paint Bright Blue bonnet removed from its Cobra decades ago and well stored since hanging on a wall as a decoration. I have my Ford color paint out sample from back when I had to spot repair the side stripes on my original paint 1965 GT350 decades ago and make the repairs invisible. )
I have tried several times over multiple years to figure out what car that might be. Several issues confound the research. 1) Many new Cobras spent some time in the Ford fleet for some reason or another or for some VIP or another. 2) As photographed production details that would narrow which contract series and or which shop completed the car are not visible. 3) Ford sometimes made changes to cars in their possession (e.g. CSX2004 and CSX2008) so you might stumble upon before and after pictures. 4) Fleet cars returned to Shelby inventory tended to changed for all kinds of reasons including repairs and reconditioning after return to Shelby American.
What I have kept a watch for is any documentation that Ford tested Firestone® brand tires on car number (?).