It depends on if you have a six or v8 and how far you're going with it. To take full advantage of the sweet package, you have to change the rear-end gears to match the overdrive tranny.
The stock 3.00 doesn't work well with the OD 5 speed. You can get better gears for the 8 inch, but the one in the six will have to be upgraded to a 8 inch too.
You also need a new cross member, drive-line and cable clutch. With all that and the transmission, your looking at 2 or 3 thousand dollars.
1965-1966 Mustang Small Block Complete T-5 Conversion Rated at 450hp Includes transmission - If you're changing over from an automatic, you will need the pedal parts here!
$3879.95/kit from Dan B's link
The six gets decent mileage, so it's not worth the price for a couple more miles to a gallon.
ON the V8, it's usually a complete package with built motor, disc brakes and the 5 speed tops it all off with decent mileage while allowing you to runs some low acceleration gears like 3.73's.