Hmm... If the noise is coming from the output shaft area when you spin it inside the sub trans i would think it might be the drive sprocket bushings making the noise.
But, before we explore that option... You removed the jack shaft correct? The small shaft in the sub trans with the gears on it? I wanted to be sure your only spinning the drive sprocket on the motor output shaft. The main noise makers that i have come across in these 125M's is worn bushings in the drive sprocket, the sprocket the chain goes around and rides on the outside of the motor output shaft, also the three roller bearings in the sub trans, two in the cover and one in the case side that the jack shaft sits in.
Does the drive sprocket have play in it? If you can wobble it and/or that oil seal around it is leaking and you have a lot of oil buildup around the drive sprocket then chances are the bushings are shot. It makes kind of a dragging grinding noise when they wear out. But so do the bearings in the sub trans.
If its shifting in and out of gear and not dropping out of gear or anything weird like that, just the noise, then the shift drum stopper and clutch should be fine on the other side. Wouldn't hurt to get a gasket set though so you can pull the right cover off and inspect the shift drum stopper and clean the oil screen as well since it hasn't run in years. You can also pop off the cover on the clutch and clean out all the accumulated sludge from the years as well.
Main thing is to figure out exactly which part is making the noise by the questions i asked you first.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....