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According to the following site,
Ford anti theft light flash code 31, means incorrect code to diesel smart module.
Is this a diesel? Or alternative fuel with a control module?
Do you have access to diagnostic equipment, as electrically the on-board systems will now think they are the other car, in which case you need to program the module in that is still with this car or change it from the other one.
Let me know the full details and I will dig further if needed.
If will double check for you shortly but it would appear so unfortunately, you likely will need the details of the vehicle the parts came from also.