Does the vehicle start? If not you'll have to re program the keys . You'll need a minimum of 2 programmable keys. Which you'll be able to do through the tool. But I'm pretty sure you may have to pay a subscription to used the fmp software in order to write the vin. You won't be able to do it on the tool, you'll have to use a pc/laptop.
Look on your tool, and see if there is a programmable module installation tab .. Probably under hot function. And see if there is an option for PCM. You may have to do a parameter reset as well.
If you can't find any of those options on the tool, go to the ford website ... Pay the sub scription , and you'll be able to do all of that through the fmp software.
Make sure you have 2 programmable ford keys!
Make sure you are connected to the Internet.
Make sure you have a battery maintainer connected.
Please anyone correct me if I'm wrong.