Ok, here we go. Kept searching untill found this in "73 CT3 & shows nothing, but can still see what looks like circlip grooves in the shaft. Be careful as think i'm right but happy to be proved wrong & don't want you to damage anything. Can you see a circlip as must be visible if there. 

Would a bearing puller work?
www.screwfix.com/p/bearing-separator-puller/19315

Just looking & looking & the shaft number is the same on ct1 & ct2 but no circlip on ct2.

www.mrcycles.com/oemparts/a/yam/500414e4...c784108/transmission

www.mrcycles.com/oemparts/a/yam/50041663...c784763/transmission

click links above is easiest way to compare.

PETE-RT1 that puller would be in with a chance for sure if you could get it in back to front with the flat side against the gear teeth but don't think there's enough deeper down to bite on. That's "if" there's a circlip in there & my way won't work. I use one of those all the time to get crank bearings off but just smack it down behind the bearing & taper side gets them off.

Not sure if you're in the US but there is a new shaft on ebay for $14. Item# 

373511994744

That's a bit of a bargain. New gear & new shaft, gotta be good.

Understood about new shafts, but then I would need to get ALL the gears if I can't take this thing apart.  I did see where the diagrams are different even though they show the same shaft. I took some closeups but can't  see anything between the gears....but you would think there's something because they don't spin like they are riding on each other (circlip on other side of stack is plainly visible). I will try a bearing separator tool to get the little one off and then truth will be told.  The separator style tool may be the trick.
Joe

I can't see a circlip after the stack [talking #6] expanding the pic, & wouldn't expect a circlip there. I'd think it would spin against the end of the splines with little gear pressed up to about 5 thou for running clearance to #6. Get a feeler in there & see what you come up with. My guess for the night!!.