There are companies here selling the kits that make putting a 5 or 6 speed possible, but I think it goes beyond just finding a T5 or T56 from a junker.
Needless to say, finding a donor Mustang with a 3 or 4 speed transmission would be simplest - you just swap over everything you need.
For the 5 speed route, check out
www.keislerauto.com to start with.
A lot depends on how much torque you plan to send down the drivetrain, and whether or not its a V8 or an I6.
If you're good at fabricating transmission mounts, adapter plates and so forth, its certainly possible to do the whole thing yourself.
You're also going to need to pull out the existing rig under the dash and replace it with the clutch pedal version, of course. Not an easy task, but doable if you take your time. Take pics before you tear into it, and as you go, and label EVERYTHING. Getting all those cables, wires and tubes back where they belong is tedious, but it can get nasty if you aren't careful.
Its possible that a Falcon clutch setup is interchangeable with the Mustang, but that's not something we see over here (I'd check with some locals who might have done the swap, if you can find them - maybe a local car club?).
1969 mustang automatic to manual transmission swap 
