Hmm, hate to say it but personally think 25 thou is too much. See what the knowledgeable say, keeping in mind the flat bearing tiny rollers standing on end. Also be sure end play isn't just basket movement separate from the cast steel center where clearance is important. I'm sure ya onto it.

The first washers that go on do not fit over the tall spacer so they do not affect the "end play" of the basket.  They affect the alignment of the gears.

Only washer that affects the end play is the thin one that goes on just before flat bearing...  and you don't really want to leave that one out. 

I'm sure some of the end play i'm measuring is in fact bonus slop back and forth on the shaft and whatnot. Everything is now accounted for and installed, and it all works properly. Gears also line up nicely - that's the first thing I checked when the previous owner suggested a washer was missing by the bearing. Thanks again for the help. 

Glad it's working great! That's the important part!

It's hard to diagnose stuff blind at a distance... so you learn that paying attention to reported details are important. For example if you have the nut tight, the spacers, inner hub, and nuts should be clamping the shaft to the inner race of the ball bearing in the case so there really can't be any significant endplay in the shaft... unless the bearing is toast? And that's not likely. (I don't what your basket end play is... but as long as you didn't leave out the flat bearing or the thin washer that goes on just before the flat bearing, or the larger OD washer that just fits over the shaft and goes on just after the flat bearing, you should be fine.)

These comments are not a criticism of you or anyone else... I've just seen so many posts where someone says they did this or checked that or this is doing that... and when the problem is actually solved 13 pages of posts later it turns out to be something simple that was mentioned right at the beginning. That didn't happen here of course. It does happen though. So when someone says something that doesn't make sense to me, I question it. Most of the time I just didn't understand what they were saying.

Check out Dale Sweger's youtube videos...especially this one:
"Yamaha CT-3 clutch side install and adjust"
I recently buttoned up my clutch side after a complete (but 2 yr long) engine/tranny rebuild and he always had some valuable insight. Hoping to ride the thing by Summer!
Joe
'70 CT1B