Remove the main shaft nut --

This nut is right hand thread and usually requires heat and leverage to remove (see the last picture in the "Holding the gearbox" section).

Remove the kickstart spring --

• Using a screwdriver, move the spring hook part way from the inner case down the stud. Hold the end of the hook with a pair of vise grip pliers and gently lift the hook from the stud and ease it counter clockwise to the edge of the case.
  

• With a screwdriver pry the spring tang out of the hole in the kickstart shaft. You can now slide the spring off the kickstart shaft.
  

Remove the inner case --

• Remove the seven nuts from the studs in the gearbox shell -- five nuts inside the inner cover and two outside the cover.
• Using a rubber mallet, tap on the sides of the case, tapping the case away from the shell. After several taps you should see a crack in the seam. When the crack is thick enough to get a narrow, thin putty knife blade in the crack, you can move the putty knife blade around the case separating the gasket from one side or the other. After you can get the blade completely around the case, except for the two locating dowels. When removing the case, press in on the kickstart shaft, so it stays on the layshaft.

Remove gears and shafts --

• Remove the kickstart shaft.
• Unscrew the selector fork spindle.
• Remove 1st gear main and 1st gear lay.
• Remove 2nd gear main.
• Remove 2nd gear lay and its selector fork.
• Remove 3rd gear main and its selector fork.
• Lightly pull on the lay shaft. One of three things will happen: 1) the shaft and bearing will come out of the shell. This is not good, because it means the bearing has probably been spinning in its bore. 2) the shaft and inner race come out of the shell. This is fine, because it means that the bearing is a roller bearings. 3) the shaft will not come out. This is also fine, because it means the bearing is firmly seated in the shell.
• If the lay shaft did not come out, apply heat to the back of the shell behind the lay shaft bearing and pull the lay shaft out after enough heat has been applied.
• Remove the clutch locating circlip on the main shaft just outboard from the countershaft sprocket. I find it very difficult to remove this circlip using circlip expanders. I end up using a pair of needle nose pliers and a screwdriver to pry this circlip off, destroying the circlip most of the time, but it is a good idea to replace this circlip anyway.
• Remove the countershaft sprocket lock screw.
• Remove the countershaft sprocket lock washer.
• Remove the countershaft sprocket nut. This is a left hand nut.
• Remove the countershaft sprocket.
• Remove the main shaft.
• Gently tap on the end of the sleeve gear with a rubber mallet, and the sleeve gear should come out of its bearing. If not, apply some heat and remove the sleeve gear.
• If the sleeve gear bearing came out with the sleeve gear without applying heat, this is not good, because it it means the bearing has probably been spinning in its bore.

Remove the cam plate and related parts --

• Remove the domed nut holding in the detent plunger and spring.
• Remove the two bolts holding in the cam plate and the quadrant.
• Remove the cam plate and quadrant.

Remove gearbox bearings --

If you were unlucky enough to have one or both bearings loose in the gearbox shell, how to fix loose bearings will be addressed in the article, Assembling the Commando gearbox.

• Remove the mainshaft bearing spacer.
• Pry out the mainshaft oil seal.
• Heat up the gearbox shell with a torch or in the oven at 300 to 350 Degrees Fahrenheit.
• Gently tap the shell upside down on a piece of wood and the bearings should fall out.
• If you have a stubborn mainshaft bearing, you can press it out from the back side with a socket that just fits into the hole.
• If you have a stubborn layshaft bearing, you will have to use a bearing slide hammer, pictured below.
• The main shaft bearing in the inner case can be removed by heating the case and pressing the bearing out with a socket or drift.

Thoroughly clean all parts --

• I have a parts cleaning tank that I soak and clean everything prior to inspection. You can use contact cleaner to clean all your parts if you do not have access to a parts cleaner.
• Make sure that you remove all the gasket material and old sealer from the sealing edges of the gearbox shell, inner case and outer cover. This must be done in order to get proper sealing when you assemble the gearbox.
• After cleaning the gearbox shell and the inner case, I normally bead blast these cases using glass beads. I then thoroughly clean the cases again making sure all the beads are removed. I then will paint the outside of the shell and inner case.
• I normally have the outer cover professionally polished or if not in bad shape, polish it myself.

Inspecting the gears --

• Inspect the gears for wear on the teeth. This usually shows up on the drive side of the smaller gear of a gear set. The above picture shows what wear looks like and I would replace all three gears. I replace gears in sets (i.e., if the 1st gear main is worn, I would replace both 1st gear main and lay.) Gears wear together and it is not recommended to mate a used gear with a new gear for they may have a tendency to wear faster. After saying this, I have seen lots of owners replace only one gear and have not heard of any disasters, especially if the bike is a weekend putt and not a daily rider.
• If the wear is only on a couple of the teeth and only on part of the tooth and not as deep as the left gear in the above picture, you could probably get away with reusing that gear.
• Check the inside of the 1st gear lay and make sure the notches that the kickstart pawl fits into are not rounded and will hold the pawl when kicking.
• Check that all the dogs on the gears are not broken or extremely worn.

Inspecting the kickstart shaft --

• If the kickstart pawl is worn, as in the above picture, I would replace it.
• The splines that the kickstart arm fits around are worn in this picture, so I would replace the kickstart shaft.

General inspection --

• I normally replace all the bearings to be on the safe side, but if you are going to reuse any bearing, make sure there is no roughness when you spin the bearing after you have thoroughly cleaned the bearing.
• Check the bushing inside the gears for wear marks and that they do not rock excessively on its shaft.
• Inspect both shafts for wear on the splines and excessive run-out. Also check the threads on the mainshaft to make sure they are not damaged. I check run-out on a lathe with a dial indicator.
• Inspect the gearbox shell, inner case and outer cover for cracks or damage.
• Generally inspect everything else to see if there is excessive wear, chipping, or damage.