OK> its a bit detailed, but its relatively easy. You have some choices.
The security system you have is called FORD PATS. (start your googling here).
1. If you have two keys ( unique codes) that are known inside the computer, you can just insert one, then the other, then the 3rd you have cut at your hardware store $10, and you can repeat up to 8 keys. Sounds like you have to take a different route. (This process is documented in the owners manual). Same thing for the "remotes" or key fobs.
2. If you have only 1 key. This is what I would do. (More advanced)
Order FOREScan, and the OBDLINK MX+ ($140). This when used with your phone, and the ForeScan app ($12/per car) for advanced diagnostics will allow you to get close to a dealer level
scan tool at your fingertips. It will allow you to get into the PATS security computer, and add keys, and door combo lock codes. This is the best OBDII
scanner I have ever used, and with the $12 advanced FORD software you can trouble shoot any issues your car may have in the future.
The other option is to spend $120 in labor, to get that 2nd key at a dealer. Then go to the locksmith, or (hardware store) to get additional keys cut. $3-$10 each.
The other option: Not recommended: is to get a "Cloned Key" at a locksmith, that will be an exact duplicate of the key you have now. This Cloned key will not satisfy the PATS computer, to qualify as 2 keys known by the computer, as it thinks you just put in the same key twice.
I would go with option #2. Buy Remote Fobs (with the same number of matching buttons you have now, or "4" for Town cars. Then also buy OEM Keys, with the Lincoln Logo on them. Buy this all from Ebay, Remotes are $10 each, and OEM Keys about $12 each. Then you have them cut for $3 each, at your locksmith. Or get a few house keys made at home depot, and chat up the person helping you, then say, I have these two car keys, can you throw them in your machine and cut these blanks I have... they will not charge you, as they only inventory their key blanks.
Here are some of my notes I dug up for you:
40 Bit Ford/Lincoln/Mercury Securilock Key Programming:
SecuriLock - Wikipedia
80 Bit Keys are backward compatible with the 40 bit system.
FORD “PATS II” Passive Anti Theft System:
Can I program a second key myself if I have one working key?
No, Preferred Option: Call or go to an Automotive Locksmith and they will have to connect a special computer to your vehicle to program the second key. Do not let them “clone” you key, as the computer will only know there is one key, seen as the same key.
Can I program a third key myself if I have two working keys?
Yes, once you have had the new key cut by a Locksmith use the following instructions.
1. Insert an existing working key into the ignition cylinder.
2. Turn the ignition cylinder to ON (RUN) and wait for “THEFT LIGHT” to turn off (3 seconds), then turn key back to OFF.
3. Remove the existing working key and, within five seconds, insert a second working key and turn it to ON (RUN) wait for “THEFT LIGHT” to turn off (3 seconds), then turn key back to OFF.
4. Remove the second working key and insert the new key before ten seconds have elapsed and turn it to ON (RUN). Leave it on for 1-3 seconds and turn back to OFF. Let it sit in the ignition for 30 seconds.
5. Repeat Step #5 for another key, and subsequent keys.
1995 - 2006 Panther Key FOB
CWTWB1U311OE #: 3W73-15K601-AA SKU: FORD-748
1. Turn ignition from OFF to RUN 8 times within 10 seconds, with the 8th time ending in RUN.
Door locks will cycle to confirm programming mode.
2. Within 20 seconds press any button on first keyless remote. Door locks will cycle to confirm programming.
3. Within 20 seconds, press any button on second keyless remote. Door locks will cycle
again to confirm programming.
4. Turn ignition to OFF. Locks will again cycle to indicate end of programming mode.
