So I just went thru this with my new motor build. There was a thread in the old forum about this. Here is the long and short of it.
1. You have the wrong mainshaft. (the one with the clutch basket on the end of it. The correct one is from a 96-97 cr125 pn#
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2. The shafts from all other 6 speed years are too short (the gear on them is 1.5mm too narrow.)
3. The 99-2002 cases are wider and thus require the wider/longer shaft.
4. Some said you could shim it but for 80 bucks, just put the right shaft in there.