I am almost done with this; you do not need to change the pedal box if you get the right pedals. The auto box has a hole for the clutch master, which is occupied by the wiring for the auto. When you pull the wiring, you free up space for the clutch master and it just bolts right in.
For the pedals, I know pedals from a Bavaria will work. I think mine came from an e12.
Once you get the right pedals, you remove the auto brake pedal return spring, unscrew the bolt connecting the brake pedal to the brake booster, unscrew the nut and bolt that the pedal hangs from, pull it through the brake pedal and out of the pedal box. The auto pedal will drop right out. The clutch pedal and new brake pedal both hang from this same bolt; simply line up the pedals push the rod through and fasten it with the nut. Obviously, you need a return spring for the clutch pedal and the bolt/nut/bushings to connect the pedal to the clutch slave.