Just replaced the alternator and belt, now I am getting a P1260 PATS code on 1999 Mercury Sable

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Could it be a bad crankshaft sensor causing the P1260 code?
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No, this is a vehicle theft code. It may be a faulty ignition key. If you have another key, try that one instead. Disconnect the battery and wait about 15 min. then reconnect and try the key. You may have to tow to a dealership and have them reprogram the security portion of the PCM.
Yes, I tried both keys already and have unhooked the battery for lengthy periods of time. Really just can't figure out what would have caused the PATS to trigger.