Thanks for that Peter, my Bike is a 2011 and so it doesn't have the rod to hold the clutch basket in place.
The good news is that I have managed to get it all back together and it works :-). Along the way I learnt a few things.
My main problem was that I would install the gearbox with the 5 screws finger tight. Then I would test the gearbox by sliding the sprocket onto the end of the shaft turn it whilst clicking up through the gears. However I hadn't installed the collar between the sprocket and the casing. The secondary shaft would then move in and when I changed gear again everything would bind up. I would then take it all apart and try again. The problem was right before my eyes, but I just couldn't see it. After posting to the forum, having a coffee and talking the issue through with a friend then it became clear. So the moral of the story is never click up and down through the gears without installing the sprocket collar.
Whilst on the bench I also noticed that the centering spring under the roller was slightly off and this had the effect of not allowing the rollers to return to the correct position between gears. A slight turn of the centering nut fixed that.
When installing the clutch I had to put a piece of wood across the top of the clutch basket and tap that with a mallet until everything was seated.
The vibration the bike had a week ago is also mysteriously gone. That worries me, but the bike is riding great again.