It really depends on the color and if it's been parked indoors or outdoors. I removed my stripes about a month after picking it up and no fade marks, but it was new. What color is the 2016? I'd think a lighter color would be less likely to show any fade marks. I'd likely pull just one piece off where the fading would be most noticeable (top of trunk lid/ hood/roof) to see what it looks like? You can purchase the individual stripe pieces from Ford, but they are expensive.
By the way, welcome to the forum and please post pics when you get your new GT350 home!