3rd and 4th gear issues

sounds very plausable. I would have suggested the same thing

You should also very much consider that you have bent the input shaft. This is something that would cause issues such as you stating. Sounds like its less of the clutch flywheel and more transmission.

I totally agree Saki. But JHM have my stock clutch as an exchange item. Regarding a bent shaft, I have already thought of that and checked the original gearbox and the new one I have fitted. The problem has been there since the first fit. Regarding bleeding the hydraulics, I have replaced both cylinders and bled the system several times BUT I would say I still have a feeling its clutch release movement related. I have cut a hole in the bell housing so can see the clutch movement and the release bearing is moving a good 1/4 inch. I can also see that everything is running perfectly true. Nobody has been able to tell me how much movement I need to clear the friction plate. I have put the whole assembly on the press and I believe it needs nearer 9mm (3/8) to get things clear but how do I achieve that?