That isn't the balancer shaft, it's the gearbox input shaft (where the clutch fits). The balancer shaft and drive gear is the one above and to the right.

AFAIK there is no "end float" measurement mentioned by Yamaha, but a little is normal to allow for expansion/contraction as the engine warms/cools. It is difficult to tell how much you are moving the shaft in and out. Have you measured it?

Most bikes I've had that have gearbox shaft end float figures given tend to be in the 0.05-0.15mm region.

One question you might find difficult to answer now with the bike in pieces is, does the rattle/knocking sound go away when the clutch (lever pulled in) is disengaged?

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