The motor is the last thing I'd be worried about breaking. It will handle it.
Halfshafts
Transmission
That's where my guess would be for the first things to let go.
They'll do the Whipple one it's the exact same thing.
The stage 2 has a much better tune, smaller pulley, bigger throttle body
You could call whipple and ask if you can just add it after the fact
https://whipplesuperchargers.com/i-2678-s650-mustang-stage1-stage-2-upgrade-kit.html
The media said:
Ford reports that the addition to the spoiler is effective at speeds as low as 30 mph and encourages drivers to experiment at the track with and without the Gurney flap installed.
Basically...they have encrypted/signed the system so if you don't have the keys to sign/encrypt the new calibration the car won't run. Much different than before so that they can do over the air updates etc. companies like Whipple were given permission by ford to create tunes that are...