You probably had Fords PATS(passive anti theft system) in both the '99 and the '00 ECM.
PATS system:
PATS keys have a built-in RFID tag, these need no batteries
There is an RFID reader around the key switch
There is a PATS module above the glove box(Rangers)
The ECM/PCM is connected to the PATS module
When you insert the PATS key into the switch the RFID tag number is read and that number is passed on to the PATS module that compares it to its "tag list"(up to 8 tags can be stored, oldest tags are erased as newer ones are added)
The PATS module was "synced" to the PCM at the factory so they can "talk" with each other, the PATS module informs the PCM either that a valid tag is being used or a valid tag is NOT being used.
PCM then either starts fuel and spark or does not.
Some PATS also allow or don't allow NSS(neutral safety switch) signal to pass, this would disable the starter motor as well as spark and fuel.
So yes, swapping out the ECU/PCM would require a Dealer to resync the PATS and PCM and also if you lost original keys then they need to add 3 more keys.
You want at least 2 working PATS keys, that will allow you to add a 3rd PATS key yourself, so by having 3 working keys if you lose a key you will still have 2 so you can add a 3rd(backup) without getting a service charge by a Dealer.
To "resync" the units you need the Ford PCM programmer AND a subscription to the Ford data base.
While they are doing this have them update the PCM for best operation, PCMs get updates just like any computer software it is just that they are rarely connected to get the updates.