You would have to use a 94-95 5.0L T5 or get another 94-98 V6 T5. You can use the 99-04 V6 T5 in your car, but you will have to either swap tailshaft housing and output shaft, or modify the 99-04 tailshaft for the speedo gear and use your tailshaft housing.
Im actually running a V6 T5 from a 95 car in my 95 Cobra. Holding up fine behind a typical 300rwhp heads/cam/intake 306. Being used for now till I get something else (maybe an Astro A5 or Tremec 5 spd).
The V6 T5 (94-98) have a torque rating of 265, which is the same as the T5 found in the 5.0L V8 Mustangs from 86-89.
Check this link for more T5 info, such as gear ratios and suggested torque ratings.
http://www.allfordmustangs.com/Detailed/349.shtml
As far as the 99 up rear end, I'll assume you are going to an 8.8? And yes it will bolt right up and yes they are wider/longer.