The biggest problem that you will encounter is adapting the engine management system of your 04 car to run the 89 engine. This swap is easier, and makes more sense, on the early SN95 Mustangs.
If you have a V6 engine in your 04 Mustang, it only has 17 less horsepower than the 1989 supercharged Thunderbird engine.
It seems like a good idea, until you start doing the numbers on the cost, and the time involved for a very small gain in performance.
It would be much easier and less expensive to swap in a 4.6 V8. It will be more powerful and reliable.
Better yet, just find a decent GT for a few thousand, and toss a supercharger on it!