From the PCM's point of view there isn't a difference between the 1999-2000 Windsor and the 2001+ Romeo providing the original induction, ignition, exhaust and wiring have been used. The motors as an assembly are the same.
Note I said the original...... So if you start mix/matching parts, then the above statement may no longer be true. For example, with the 1999 PCM if you use the larger fuel injectors of the later MY, then obviously there would be some effect of the larger fuel injectors.
OBTW, the motor currently in my 2000 GT came out of a 2003 Grand Marquis. So I have actually done the Windsor to Romeo swap. That was 3 years and 45K miles ago.
2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.