The gear box oil pump runs off the back of the clutch basket.

Not good its missing. You will need to strip the box down and make sure its ok. I think I have a few spares of them kicking around though.

There should also be 2 needle roller bearings in the clutch hub. That won't of been doing anything any good if one of them was missing. I'm sure I have a few of them kicking around too!

Yes there should be a ball bearing on the end of the clutch shaft, under the top hat.

There are also dowls behind the transmission plate. If I recall 2. These locate the plate into the crank cases. It might well be one of them.
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If I have to take the carbs off once more...