I've been thinking, usually not such a good idea. But do you think that maybe the part you are having trouble with is somehow related to it being the input shaft? The front bearing on this shaft is not seated the same way as the others. The collar of the inner bearing race against the bearing is a different standard than the outer races of the other bearings?
I've been thinking, like I said, but I can't make any magic from this.
Does this somehow have bearing on the variation?