If you get actual Lincoln remotes through ebay (as opposed to any of the BS aftermarket "clones" that never work right), here's the procedure:
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"REMOTE TRANSMITTER PROGRAMMING
NOTE 1: All remote keyless entry (RKE) transmitters must be programmed at the same time.
NOTE 2: Programming (or reprogramming) of the RKE transmitters can be accomplished using a diagnostic tool or by carrying out the following steps:
The vehicle must be electronically unlocked before entering program mode using the RKE transmitter, RKE keypad (if equipped) or door lock control switch while the driver door is open.
Turn the key from OFF to RUN 8 times within 10 seconds, with the eighth turn ending in RUN. If the module has successfully entered program mode, it locks and then unlocks all doors.
Within 20 seconds, press any button on an RKE transmitter, and the doors lock and then unlock to confirm that each RKE transmitter is programmed.
Repeat this step for each RKE transmitter.
Exiting the programming mode is accomplished if one of the following occurs:
The key is returned to the OFF position.
20 seconds have passed since entering programming mode or since the last RKE transmitter was programmed.
The maximum number of RKE transmitters have been programmed."
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The maximum number of remotes for one car is 4, if you care.