So either it isn't plugged in fully to the port (I've found it tight the first few uses) or the tool is defective.
Edit, can you send a pic, taken from the floor looking up, of the tool plugged in the obd port?
It isn't a hard install at all. Something is off.
Did you check the obd port like someone suggested? I assume you have the car keyed on to the run position. Don't forget to keep the car on a trickle charger too.
In the end, take a breath and call the ford help number. It's unlikely, but...
I won't start a track day with less than 50% on my oem pads. I keep the old ones as back up and the price of OEM pads has dropped a lot.
New performance pack pads are 10mm of friction material and 0.25in backing plate.