First off, there cannot be just one key stored in a '99 Mustang. The little bit of information that you have provided points toward using the wrong protocol...again. And once more I would advise reading the manual that came with your programming devise, preferably before you start, to prevent placing yourself in this situation in the future.
I would also recommend submitting an application to join Keypro, assuming you are a legitimate locksmith. Once verified and accepted, you may ask for and possibly receive the technical advise that our membership cannot discuss in a public forum such as this.
- Jim Hetchler, robk2, n7lima and 2 others like this