T56 in a NE is a pretty much bolt in affair as long as its setup for a Mustang like a Terminator trans or (better) a wide ratio magnum. You need a T-56 specific crossmember and the hybrid u joint/shorter driveshaft and that's really it. Be aware that the termi trans which is a close ratio T-56 has a 2.66 first gear vs the 3.37 first gear in a Mustang GT. This means that you need to be making enough torque to use that first gear or run MINIMUM 4.30s out back.
The only real benefit to a T-56 is 5th gear, yes 5th, not 6th. 6th is a .62 overdrive, which is what the 5th gear in all 02-04 3650s is and the .68 5th gear in everything prior to that is very close as well. Unless you need that extra gear between 4th and overdrive, I'd get a well built t45 or 3650 before I went with a T-56.
2000 Mustang GT Steeda #0048
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.