Quick update and thanks for all the comments. I should have said from the first post that the clunk was pretty much definitely from the gearbox (should never say definitely, about anything to do with this bike I know) as it goes into gear. I have checked the cush drive nut and it is at 65lbs per square inch. I think I have found the trouble I was having with the SRM new clutch plate, I had followed the instructions given for fitting it but made a mistake or misread the bit about offering up the pusher and roller bearing. I put the pusher in the pushrod hole, having removed the pushrod from the gear-lever side, then put the clutch plate on and wound in the 4mm allen adjust thinking it would abutt with the pusher, it didn’t, it wouldn’t go in far enough. I checked with SRM who told me this was alright and just go ahead and cut the push rod to length and set it all up.
The trouble I had when I did this was that the hole in the Allen key adjuster did not line up with the pusher. This resulted in cutting the pushrod to slightly the wrong length and I assume the problem with getting the springs and cone nuts on.
Anyway it’s all good now, just need it to stop raining so as I can take the bike for a spin to get the clutch pressure right before the out cover goes back on. Fingers crossed the the clunk will have reduced.