Unfortunately some of the above information is not correct. Installing a 4.6 in an SC is going to be a bit of a pain. The entire wiring harness from an SC is different compared to a 4.6. Even in 94 when both the 3.8 SC was offered as well as a LX 4.6 the two wiring harnesses are totally different. It's like they are two different cars.
Physically speaking the engine mounts and K member changed in 93 to accomodate the 4.6. You will have alignment problems if you try to put the 4.6 in an 89-92 SC. Using Tbird 4.6 mounts on a 93 or newer SC makes it physically a bolt in operation as far as the motor is concerned.
Keep also in mind that the bellhousing is different from a 4.6 to 5.0&3.8 so you will not be able to interchange the transmissions. If you intend to use a Mustang 5spd, then you will have to deal with a shifter that is too far forward in the console as well as possible issues with driveshaft length.
It's not as high tech to put a 5.0 stroker in the car but you will find that it is much easier and there is a lot more room left over in the engine bay.
Either way if you want to exceed the performance capabilities of the V6, forced induction or a lot of nitrous will be necessary.
Oh, and love the "other" car. I used to have one myself.