The following instructable goes over replacing the throwout bearing with the engine and transmission out of the bus. If you haven't gotten that far go here: Engine removal instructable
I'll also go over checking the transmission fluid and replacing the starter bushing.
Step 1: Tools
Flat head screw driver
17mm socket & wrench
17mm box wrench
15mm box wrench
clutch alignment tool
transmission drain plug allen socket
80W90 gear oil
Step 2: Splitting the Two.
1. Remove all four 17mm fasteners that hold the transmission and engine together
2. Split transmission and engine apart making sure both are fully supported.
Step 3: Out With the Old and in With the New.
3. Un-clip the springs that hold the pilot bearing in place with a screwdriver.
4. Put the new throwout bearing in place and refasten the springs.
5. Add a thin coat of universal grease to the end of the input shaft.
Step 4: Checking the Transmission Fluid
1. Level out the transmission
2. Remove the fill plug
3. Insert finger into fill hole. Oil should be at bottom edge of fill hole. Add 80w90 gear oil if needed.
Step 5: Replacing Starter Bushing.
1. Remove starter. This will help with mating the transmission and engine later on anyhow.
2. Punch out bushing from rear of bell housing.
3. Press in new bushing
Step 6: Mating the Transmission and Engine
1. Use the clutch alignment tool if you have one to make sure the clutch is still aligned.
2. Push the transmission back into place.
3. Add a little universal grease to the end of the starter shaft and re-install.
4. Torque down each of the four 17mm bolts.
Now you're ready to re-install that engine.