Here's my list:
Auto/manual conversion checklist:
Manual tranny
Flywheel and bolts
Clutch kit (and pressure plate bolts)
Driver's side mount for manual
Shifter assembly
Shifter cables
Clutch pedal assembly
Brake pedal (or grind down your stock one)
Clutch master cylinder
Clutch slave cylinder (if not included with tranny)
Clutch lines
Manual ECU or wire in resistor box for the auto ECU ('96 and newer (OBDII) only)
On the AE92 it's pretty easy. THe stock axles work, the hardest part is swapping the tranny out and drilling the master cylinder hole. With the wiring, all you need to do is run the wires that used to go to the neutral start switch to the clutch start switch on the clutch pedal.
-Doc