ahh yes, ive palyed with a T5 on my 94 stang.
Your stock flywheel will need to be viewed, if its in "good/usuable" condition, it can be resurfaced and work just like new (basically the same principle of turning brake rotors)
Depending on how it was driven will depend on its condition. Slow on the clutch causing longer friction time will cause heat damage and warp things for example.
As far as remove/install, pretty simple IMO. Even though im not done with the install Yet :p.
Pull the T5 out, and remove the bell housing, lots of extension and wobble joints is nice for this, reaching the top 2-4 bell housing bolts SUCKED. I had to undo the Y pipe in the exhaust to help bring the engine downward to me.
Anyways from there you'll remove your clutch and flywheel ect ect ect. While you are down there !!! Replace the rear main seal. Cheap Quick, can be PITA, but they are tedious about leaking over time on any vehicle. Definately a smart change out.
Last I remember on my old 94 was getting the clutch cable back on wasn't so easy, idk if I was doing something wrong or what ...
With good help, all tools, and pre reading up on it, you should definately do it in 2 days.
There is an alignment tool you will want for putting the clutch assembly in. Sorry its been a while since Ive done all this so I cant remember names and such for sure.
Not that this is the one you need, but this is the alignment tool I speak of