[DougD]

FatBoy
I just went through this myself. It can be confusing.
The original trannys were big input Toploaders with the short tailshaft. Putting one together today, you can use any of the various short tailshafts. You may find examples with either the mid or rear shifter mount, or both.
The shifter assembly mounts to a plate which is bolted to the tailshaft. This plate must match the holes on the tailshaft, mid or rear mount. The 427 Cobra needs the shifter in the rear mount location.
If you don't have a shifter yet, you may want to explore that a little to be sure everything will bolt up properly.