Whaler,
You are correct - the shifter is indeed out of a 1965 Mustang. Given that the engine/transmission were moved aft in the Cobra, Shelby simply undid the two bolts and flipped it 180 degrees.
The Mustang toploader uses a different bolt pattern than the TKO, so you have to get the reproduction for TKO piece. They also make a reproduction shift knob that has the 5-speed pattern on it instead of the original four.
Sacramento Mustang has both of these parts available. (
www.sacramento-mustang.com)
Brad