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Got a strange problem with my shimano rear thru axle hub.
On the non-drive side there are 15 bearings in a bearing retainer, no issues, but on the drive side there are 16 loose 5/32" (measuring a bit smaller, 3.92mm) bearings that tend to go on top of each other as the axle rotates even though it's tightened down - this is what I believe generates the intermittent clicking noise.
Removing one bearing seems to make it a bit better but it's still rough.
What to do? (and why do they use such tiny finicky bearings..)
There should definitely be 16 in there. Are you sure that it's adjusted correctly?
Could the bearings be undersized? You can feel that the bearings "catch" even before you tighten down the nuts on the non-drive side so something seems off. Or might it be finicky to get a perfect "fit" when you insert the axle from the drive side?
They seem to go on top of each other no matter what i do. Could they be damaged? Hard to tell since so small.
Figured it out, turns out it's finicky: the bearings on the drive side all need to be pushed out towards the outer edge of the bearing race for the axle nut to center correctly / go deep enough into the freehub (it's not self centering and doesn't push the bearings into place itself like older shimano hubs i'm used to with larger bearings).
You know you've fitted it correctly when the drive side nut lip fully enters the freehub body like so:

Well done on sorting it out mate. I've not messed with loose bearings in hubs for years now I must admit.