Anti theft system

If you have a spare key try using this to lock and unlock then start the vehicle. If this does not work it needs to be plugged into fords diagnostic system or equivalent !

Passive Anti-Theft System (PATS) contains a theft indicator, encoded ignition key, transceiver module, instrument cluster, Powertrain Control Module (PCM), Standard Corporate Protocol (SCP) communication network and starter relay. PATS uses radio frequency identification technology to deter driveaway theft. Passive means it does not require any activity from user. PATS uses specially encoded keys containing permanently installed transponders. Each transponder contains an identification code. Each replacement encoded ignition key must be programmed into instrument cluster before it is able to start engine. Encoded keys are larger than traditional keys, do not require batteries and should last lifetime of vehicle.
Transceiver module communicates with encoded ignition key and is located behind steering column cover. Transceiver module reads encoded key and sends data to instrument cluster during each vehicle start sequence. Instrument cluster initiates key interrogation sequence when vehicle ignition switch is turned to RUN or START position. PATS uses PCM to enable or disable engine. Instrument cluster and PCM have shared security data, making them a matched pair.
PATS also disables starter motor. If instrument cluster is removed from vehicle, engine will not start. Theft indicator will prove out for 3 seconds when ignition switch is turned to RUN or START position. If PATS is malfunctioning, theft light will flash rapidly or glow steadily. PATS theft indicator flashes every 2 seconds after ignition switch is turned to OFF to act as a visual theft deterrent. PATS will not store DTC or flash theft indicator if valid encoded ignition key is used and a failure occurs in starter relay circuit.

TROUBLE SHOOTING
Verify customer concern. Check fuses No. 9, 14, 16 and 28 (all 10-amp) in central/fuse junction panel. Check PATS transceiver and ignition switch for damage. Check bulbs and wiring harness for damaged, loose or corroded connections/circuitry. Check ignition lock cylinder and encoded ignition key (PATS key). If problem exists, repair as necessary. If problem does not exist, perform self-diagnostics. See SELF-DIAGNOSTIC SYSTEM.

SELF-DIAGNOSTIC SYSTEM
NOTE:All diagnostic tests are written specifically for New Generation Star (NGS) tester. Most generic scan tools should be able to perform all test procedures.

Did you check Fuse # 6 (15A) in central junction box (CJB) behind left side of dash.