A long long long time ago I rebuilt a W50 tranny in my sisters Corona after the input shaft gear and bearing were trashed.
Replaced all the bearings and the input shaft.
It had a whine until teeth broke on the countershaft.
Which is when I figured out the problem.
The center part of some of the bearings were 2 pieces. One of the pieces acted like a spacer.
When removing the bearings on the countershaft, one of those spacers remained on the countershaft. The new bearing was then installed with its spacer. So now there was 2 spacers instead of 1 on the countershaft. That preloaded the gears, causing a whine and eventual teeth breakage.
Didn't see the problem until after the teeth broke and everything was apart again.