Assuming the tuner itself will work for the year of mustang, you may have a couple options.
Did you return the truck to stock before it was taken away? If so, you can clear the entire memory and unlock the tuner with livewire software. I did this when I sold my sport trac, and received tunes via email and loaded them up.
If not, you will likely have to send it in. Talk to an SCT tuner.
I used http://www.hensonperformance.com/
and he did a good job with the sport trac, but a crappy job on my F150. Nevertheless, he could probably answer your question.