New owner of a used Mustang

Welcome! Most things are about the same from 99-04, some parts changed on the engine after 00-1/2, but most things are the same otherwise.

 

99-04 is all New Edge. Everything will work between years, some with
modifications. Late model '04s got the 3.9 V6, but it will still run in
99-03. However, the new Edge basic proportions, interior design, and
chassis remained the same as the previous model.

A split port induction system was added in 1999 for 190HP

1999–2000, while the Mustang GT's 4.6 L V8 saw an increase in output to 260HP
due to a new head design.

01-04's V6 HP was increased to 193 HP.

The 3.9, on top of the 01-04 increases, is another +3 ft-lbs in torque, with
Noise, Vibration & Harmonics improvements.

 

The only major parts that differ are the pistons and engine bore, they made some changes and refactored 3.8 to 3.9, but all other parts interchange.
It's a worthwhile project as these cars are getting scarce.