PATS(passive anti-theft system) was added to Fords in the late '90's so if you do go with a '99 ECU then yes you would most likely want to have the PATS "check" removed from the ECU.
This can be done by a programmer with Ford ECU software, $250-$400, this is not illegal if you own the vehicle, programmer's change software all the time to get more power or better MPG.
Ford dealer can do it but won't do that as far as I know, not a factory approved change.
PATS systems use keys with an RFID tag embedded in the black plastic end, this requires no batteries, each PATS key has a unique ID number in this tag.
When you insert this key into ignition and turn it on, a ring(wand) around the key slot sends a burst of RF(wireless) energy, this gives the RFID tag enough power to transmit it's unique ID number.
The ring picks up that number and sends it to the PATS Module or to ECU with PATS module built in.
That number is compared to a list of up to 8 numbers/keys that were programmed into the system at the factory.
If number is found fuel pump and fuel injectors are enabled, if number is not found or there is no number received then pump and injectors are disabled.
In later systems starter motor is also disabled.
Separate PATS module is "married" to it's ECM, so they can't be swapped around, and ECM needs "trigger code" from module to start pump and injectors.
It is a good system, no real work around.
As adsm08 said, I would look at using older ECU with older harness