There is no way to reset or to program new keys unless you have a locksmith or dealer create a new key to match the VIN number of the truck or have them erase the current key(s) and reprogram the key you have back in. However, you say you "bypassed it so it would turn over, then the key stopped working" That would likely negate any programming as the process can be messy even with everything working as it should. Ford uses the Ignition switch, Instrument Cluster, Body Control Module and the Power-train Control Modules all in the security system. If any of them get or give a bad response that the security system does not like, the system stops the truck from starting, it will also stop any programming access to the PATS system.
My first step would be to put everything back to stock with no changes or bypasses. Then you may find that it returns to starting but running poorly, but that takes any of the modifications out of the way, and would allow for diagnostics on a running engine.
Wednesday, May 30th, 2018 AT 4:21 PM