the only difference with the cobra t5 is that it got a tapered type bearing on the end of the mainshaft where it goes into the input shaft.
all previous t5's had needle type roller bearings that you'd manually insert into the end of the input, which would slide over the tip of the mainshaft.
your cobra trans now has a bearing instead that's pressed onto the end of the mainshaft. THis is shared in common with the t5z trans..(but that's about it there)
the pocket style bearing actually includes the torque rating of the trans slightly, and will also allow you to dial in more preload on a rebuild.
make sure to use the cobra mainshaft with that bearing when you rebuild your trans. You'll need a 93 cobra style input shaft though, if this is going into a fox.