Pro Racer Package - Yes!
Stock ECU - No!
The 05+ Mustang ECU is sooo indepth it would be too difficult to swap into a project car, but I have seen some use the 05+ engine and step back a year with the computer and use a 04 or older computer.
The depths/layers of Electronic Throttle Control and Returnless Fuel Stystem and Toruqe Managment and and and.
Is too much to put into another car.
You are correct though the new 3valve engine is working very well for being fairly small and still producing big numbers. One recently in Michigan just put down 700+ hp built bottom end and a big blower on it.