Hi Mark1,
Well the chain tensioner is an obvious one if you can't get the transfer shaft to sit correctly unloaded without even taking the engine into consideration.
It is most certain that you clutch body is flogged out as its an early die cast unit and with the way that piece of Key Steel is damaged it tells me that you clutch body hasn't been running true for quite some time.
You are really lucky with the chassis as a flogged clutch just invites stress fracturing into the rails and yours seem to have been spared and also your pocket for that matter, so that's a big plus towards rebuilding the twin railer.
Throw the clutch body straight into the scrap bin and organise another. There are two sizes as you correctly state, 5/8 and 3/4 with most being 5/8, the smaller size shaft diameter. BTW that key is not a Woodruff key as a Woodruff key is flat on one side with a half moon on the other. These are used on most of the sprockets and the clutch cone
/ transfer shaft joint.
Keep plodding on and don't forget to post up photos as you go as that's great for both myself to give you advise and also other members to learn from.
Cheers,
BB
