Correct Howard, the SMC (Secondary Master Cylinder) is on the left brake caliber and is unrelated to the clutch. No interconnection whatsoever.
But back to your issue...did the clutch and gear shift seem to work 'normal' in other gears while underway (3rd, 4th, and 5th, for example)?
Ok, Yes it appeared work fine in all other gears.
But that was yesterday
...It seems to be getting worse. Then better... then worse. Coming home from work last night it felt fine. Different to what it did before I started experiencing the problem in that it took a lot more pressure to go into first and I had to sustain the pressure on the lever for longer to ensure it went in but it was smooth.
Today...started the bike to move it around the yard and it took a huge kick to get it to clunk into gear.
Having said previously that I changed the clutch fluid again and felt that there was no air in the system as the rear wheel did not turn with the bike in first and the clutch in ie fully disengaged, I decided to revisit the lubricating the links idea just to make sure. I then started the bike again, a huge clunk and grate into first.
So I put it on centre stand and in first with the clutch in the rear wheel turns strongly. Too much to stop it by hand and I had to use the rear brake. Now not disengaging?
So I have now done the tests you asked and here are the bizarre results:
With the bike on the centerstand and in 1st gear (bike off), can you rotate the rear wheel by hand? Then while the clutch lever is pulled/held, can you still rotate the rear wheel by hand?
Having turned the bike off I could not get it into any gears either using the clutch or not. So I turned the bike on and put it into first and then turned the bike off. I couldn't turn the wheel either with the clutch in or out.
With bike off and someone gently rotating the rear wheel, can you clutch/gear change 1st through 5th, and back down? What abnormal sounds does it make? (it should make a single clunky noise as each gear is changed)
Couldn't try this as we couldn't get it into first with engine off.
Sorry, lots of questions, but I/we can't make out what is going on without more info (or posting audio files for us). Thx