The Ford Panther line (Town Car, Grand Marquis, and Crown Vic) did not get a PI motor until 2001+. Therefore if the donor has come from a 2000 model year then it's a non-PI motor. This means that a non-PI motor has been mated to a PCM that is expecting to control a PI motor. While I'm not 100% certain, IMO if asked to tank an educated guess, the motor will run but not make great power. The fuel curves will be wrong.
The PI verses non-PI is not the reason why the motor will not bar over.
Which fuel injectors were used? This could also be an issue because the Lincoln uses very different sized fuel injectors (the Mustang GT has larger injectors).
If this were my project I would be very concerned about the quality of the pre project advice that you got. IMO you will not be happy with the result after force fitting a non-PI motor into a car designed for a PI.
Note, the 2000 Mustang GT that I regularly drive (and have for 7 years now) has a motor from a 2003 Grand Marquis. So I can say from first hand experience that it is possible and it does work to use a long block from a PI Panther in a 1999+ Mustang GT.
Note2, it not possible to swap a Lincoln PCM into a Mustang without re-wiring the entire car. The electrical is vastly different between the two cars. This motor swap only works if the new motor looks the same electrically as the original. That's why is necessary to swap the motor's wiring harness to maintain the original.