Hey Rebel,
Just to add to the conversation and to piggy back on what eGuru stated your issue is with the interrogation of the key code to start the vehicle. So either the PATS interface module is not programmed correctly or you need a new PATS interface module. As eGuru stated earlier, start by programming the second key and then once you have both keys programmed, programming the PATS is a breeze. As eGuru stated, disconnect the 4 pin connector to rule out any possibilities of interference and test again with the key next to the ignition without inserting it into the ignition. Also, the remote start module has some fuses under a cover which, surprisingly, contains some software, I ran into an issue where this cover was not seated properly and got an unusual no start issue when remote starting. The cover has the fancy writing on it that says ford remote start which you've already seen. Don't remove the cover just yet, just push on it to make sure its seated properly.
If you end up finding out it needs a new PATS interface module I got this one off of amazon and it worked great!
-Rich