There are a few variations of the T-45.
you have 96-98 Gt's and 96-98 Cobra's. The difference between these is nill as i believe the first gear ratio is the only significant difference between the 2 transmissions. The GT's have a 7 tooth speedo drive gear while the cobra's have a 8 tooth speedo driven gear. The VSS (vehicle speed sensor) is still electronic, but it uses a "gear" to spin the VSS to recieve its electronic signal.
Then you have the 99-mid 2000 or 2001 (i forget which year exactly) T-45. These are essentially identical to the 96-98 T45s except that the VSS no longer has a gear and uses a hall effect style sensor to pickup the electronic signal for the speedometer.
Then there are the T3650's used up to 2004. I dont care how many people say "its a completely different tranny". Its STILL a T-45 made by Tremec (Borg Warner was bought out by tremec) with a few differences in the shifting mechanism and gear ratio's.
The T5 has a seperate "transmission" and bellhousing, while the T-45 bellhousing is an intergral piece of the transmission. The spline size is 1 1/16" w/ 10 splines for T5, T45 and 3650's.
Thats what i know.. way to much info. floating in my head about mustangs. lol