So, you will need something like this kit...
http://www.geocities.com/MotorCity/Downs/1966/5speed.html#dhp
For modern setup with performance go with a Kit from Dark Horse for about $3,500 this kit uses an aluminum bell housing, I would consider steel. This kit also uses a hydraulic clutch so no need for the z-bar.
1967-1970 MUSTANG AUTO TO TKO600 SWAP
TKO600 transmission with 4615 alloy gears and shafts
billet shifter
hurst handle
5speed knob
Hurst shifter boot
crossmember
Aluminum bell
blockplate
McLeod 3-piece dual-surface 800 series clutch
Ford t/o fork
roller pilot
McLeod steel SFI flywheel
bolts for flywheel
pressure plate
transmission
JMC hydraulic slave kit
transmission mount
slip yoke
You will also need a clutch pedal and your driveline should need to be shortened.
Me, I went with the classic approach and spent about the same but I wanted to go with a toploader. My car was a 390 - 4 speed, but got a 302 and C4 over the years. There are a lot of parts you will need for the classic route as well, and a lot of this stuff is not cheap and the 390 stuff is even harder to come by.
Classic route for a toploader you need the following:
Clutch Pedal
Clutch Pedal Pad
Brake Pedal
Brake Pedal Pad
Pedal Bushings
Pedal Hanger (if required)
Clutch assist spring & bracket
Rod from pedal to equalizer bar
Clutch rod boot at firewall
Clutch equalizer bar (Z bar)
Frame side Z bar bracket
Engine side Z bar bracket
Bracket bushings, C clips and felts
Rod from Z bar to clutch fork
Z bar springs
Bell housing
Engine block plate
Pilot bushing
Resurfaced flywheel
Rebuilt clutch disc
Rebuilt pressure plate
New throw-out bearing
Clutch fork
Clutch fork pivot
Bell housing boot
Bell housing lower cover (if required)
4 speed toploader transmission
4 speed shifter
Upper shift boot and bezel
Backup light switch
Speedometer Cable and Gear
Transmission Yoke (if necessary)
Transmission Cross Member (if necessary)
Transmission Insulator
Driveshaft (if necessary)