I dont really know about an EF but I did it on my XF.
I bought a wreck to get all of the parts from. I needed, the pedal box so I could mount the clutch pedal, clutch and cable, I had to buy a dust cover as it didn't have one. You will also have to get a spiggot bearing for the input shaft. The tail shaft and x-member were the same so I didn't need to get them, I had to join the neutral safety switch so that I could start the car, and also change the speedo drive gear. The speedo unit on the 4spd single rail is the same as the unit on the BW40 auto.
I'm not familiar with the EF or autos, but I'd check out first whether the computer is the same in the manual and auto, and whether the wiring is the same and can be linked up with the new box. There might be different computer maps for auto and manual, and there might be different sensors connected to the transmission.
EA S is exactly right, and on the late EEEC-IVs and EEEC-V computer controlled Falcons, the EEC controlls the transmission and the aircon and other banal chores.. I'd see if its a simple jumper setting on the computer or something to convert to A/T to manual. But i know next to nothing about the Falcon computers in a physical manner