I've heard of at least one T45 swap into a 4.6L bird. The T45 will fit the mod motor bolt pattern, but I don't know if it's really any stronger or weaker than a T5.
For the record, the T5 is a hunk of crap compared to the M5R2. The first gear on the input shaft is HALF the size of the M5R2 gear. It's a smaller, weaker box and Mustangs have a hard time keeping them together with a thousand pounds less weight to carry around. If you want smooth shifting, less radical gearing and don't plan on beating your SC up, then maybe a T5 would be for you. But if you start banging gears you better get good and rebuilding it.
Aside from the cost of the tranny, I think the LS1 T56 would be as cheap as a T5 to swap in. Once someone pulls the trigger with some good pictures, you'll see T56 SC's all over the place. Your level of fabrication would include some mods to the slave cylinder and a custom driveshaft, but otherwise the McLeod bellhousing is a bolt in, you retain you stock flywheel and pressure plate, buy a LS1 clutch disk, buy the shifter, etc...actual fabrication should be minimal.
A big hitch is you would need a 4.10 rear end just to get back to your stock ratio's with a 2.73 rear end SC.