The Ford PATS system is pretty good, so the best first step would be to set up some protective perimeter to prevent ways to defeat that. Like physically locking the OBDII port and ECU with steel covers or lock-boxes.
Then I'd put in something unusual which would prevent the engine from running, such as a means to remotely disconnect the crank position sensor, and starter motor, and fuel pump.
Throw in a few decoy switches and dummy wires too, routed where it's difficult to trace, just to give the crook an extra bad day.
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