Where the clutch cable goes, near the instection cover ? ? ? Yes, its an outer cover off job.
There could be a tight fit inside the bearing, so the nut is tight but it hasn't pulled the mainshaft enough for it to sit tight against the bearing inner race, 6 or 3 mm is a lot of difference. Is the MK3 mainshaft different in length to the Pre MK3 and a Pre MK3 mainshaft is fitted. What about if the mainshaft first gear is fitted the wrong way round, that definately gives issues with the clutch position on BSA Unit Singles.