That CAI setup is probably a hair better than stock....maybe. I would just leave it as is. The tune is what gives the most HP when you look at someone getting their coyote tuned and then tuned with a CAI. So I honestly wouldn't spend $300 on a new CAI unless you find like a JLT for really cheap in good condition and you just want to have it.
Honestly, if you know how to drive that 6 speed, as in launching it at the track, and get some MT drag radials, you'll be a low 12 second car. Depending on DA, temp and such, could see high 11's.
With my Auto with tune, JLT CAI, cat deletes, X pipe and axle back and street tires I ran a 12.4 @ 113mph with a 2.0 60'. And that was also with BMR lower control arms and panhard bar. I still need to install the upper and a few other mods. Then torque converter and DR's and 11's will be cake.
2014 Mustang GT, A6, Grabber Blue