Tremec TKO is the way to go if you're putting in a 5spd, especially if you're starting w/ an AOD. You're going to have to buy all of the same parts (clutch, etc) anyways. You might as well go w/ the TKO and be done with it.
Simply put, the TKO is the strongest 5spd tranny you can put into a street driven Mustang. The T5 vs. the TKO is a twig vs an oak tree. (If you want a crazy strong tranny, consider the T56 or a Richmond gear box, etc.)
The TKO does cost more than a T5, especially a JY T5. But you get what you pay for. Some claim the TKO is tougher to shift than a T5. This is true, to an extent. You get used to the notchy shift patern, and it does get better as the tranny wears in.
Differences installing a TKO vs T5. Off the top of my head: bellhousing (TKO sepecific), clutch friction disk (GM style spline count), slip yoke (spline count), some minor mounting and wiring differences. Since you're starting w/ an AOD, you're going to have to buy a clutch, and a bell housing, etc. So get the TKO stuff now, instead of grinding up a few T5s and then switching over.