IMHO, here's the issue....
The aftermarket tune is too rich for either the idle or light throttle accel......causing the plugs to foul...when a miss is detected the ECM will automatically raise the rpm 200+ to keep the engine from stalling then slowly bring the idle speed back down unless there is another miss detected.
IMHO, not unusual for most of the "mail order" tunes.....IMHO, go back to stock
Pretty much what I was thinking and saying. If you have no issues at stock then it is 100% the tune or intake, but likely the tune.
OP, is you tune from AM? I know they have had lots of issues in the past couple years and this symptom being one.
(11.)2012 GT500 silver with red stripe, SVT performance package, and Recaro seats.
2018 Honda Civic Type R
Past Mustangs in order and color of text.
(1.)2000, (2.)2004, (3.)2006GT/Auto traded for (4.)2006GT/Manual, (5.)1996, (6.)2011GT, (7.)2003GT, (8.)2006GT, (9)2013 Boss 302, and (10.) 2002GT
(I have owned a few non Mustang cars over the years as well, but always try to have a Mustang with it or come quickly back to a Mustang!)