Kevin, I think that you might be overthinking this. Have you put a long piece of stiff wire or a length of 1/4" inch rod into the gearbox main shaft and measured how far in you can push it? If you do that and operate the clutch lever you might even be able to feel the lever arm trying to push against the stiff wire or rod. My guess is that there is something left in the hole but there is no magic or hidden subtlety involved. It is a straight hole that requires something straight going through it. From the figures you have given it seems that there is something about two inches long in the hole.. Have you ever had the kick starter cover off since you owned the bike? There are some clever people who have made a short length of rod with a forked end which will fit over the lever arm and prevent the rod rotating and wearing a groove into the lever arm. You might find that you are lucky enough to have one of those.
On another front when I started supplying the needle roller thrust race conversion for the twin clutches I did use 7 mm diameter silver steel. The idea was that this was a nice fit inside the main shaft tunnel and would further help to prevent any tilting of the outer clutch plate. However, once the Spares Company started to stock them they asked me to keep to the standard ¼” diameter as there is a bush inside the clutch end of the hole through the main shaft. I used to knock this out to allow the 7 mm rod to pass through but it seems most people did not want to do that and so they are all provided with ¼” diameter rod now.
On another front when I started supplying the needle roller thrust race conversion for the twin clutches I did use 7 mm diameter silver steel. The idea was that this was a nice fit inside the main shaft tunnel and would further help to prevent any tilting of the outer clutch plate. However, once the Spares Company started to stock them they asked me to keep to the standard ¼” diameter as there is a bush inside the clutch end of the hole through the main shaft. I used to knock this out to allow the 7 mm rod to pass through but it seems most people did not want to do that and so they are all provided with ¼” diameter rod now.