So when rebuilding my clutch with new fiber plates I noticed the shaft has a fair amount of end play. The best way I can describe it is I can grab the clutch basket and the entire crank shaft moves in and out. Also the clutch adjustment screw is flush with the locking nut and not separating the clutch plates. It seems like the added play in the shaft makes the clutch push rod move further to reach the pressure plate.

Should there be end play, the bike is new to me but I dont recall that being a problem before, in fact the clutch slipped badly.

I guess you're talking CT3 so looking at the link the bearing is retained by a plate & will be bottomed in the case so shouldn't be side movement unless the plate it bent or the center nut undone. Are you checking side play [end play] with the hub nut

Also, you might feel some movement of the basket with big gear, like running clearance so the hub can spin when disengaging the clutch. But shouldn't be end play of the shaft by grabbing the center [call it hub]. Unless the bearing is totaled, but never seen one clap out like that. Adjuster should have roughly 1/8 to 1/4 turn off the rod [personal preference really, but not zero clearance & definitely not tighter than zero or clutch will slip.
To add. If there is 5 plastic/rubber separators under each fiber you can bin those as no use to man or yamaha. No6, not to be confused with number 15 which sits over the big gear to dampen basket chatter at idle.
www.partzilla.com/catalog/yamaha/motorcycle/1973/ct3/clutch
 

I keep adding to the story sorry[rainy day]. Clutch & crank have helical gears, so any play sideways in the bearing or how its retained will have the shaft going sideways & back depending if under power or throttling off . On one of my 360's years ago it was noticeable & could feel it while riding holding the clutch lever. I had to run plenty of rod clearance to avoid slip under power. [maybe i fixed it, can't remember now].

 
It would be great to confirm what bike you are working on...  and I'm easily confused so the "crankshaft" comment  throws me.If it's a CT3, not sure how the clutch shaft could move but as RT325 said the basket could.  Especially if someone screwed up the thrust washers and thrust bearing assembly.  Yamaha diagrams show one washer and thrust bearing and they don't draw the second washer which comes with the bearing.  So thrust bearing has a steel washer on both sides.

They also show the disc assembly order wrong in most diagrams...  exception is the engineering cutaway drawing. 

 

Sorry yes it is a CT3 and I have not had a chance to get back out and work on it since the original post.
To answer a couple questions the rubber spacers are removed to if anything the width of the overall clutch basket is less.
I am speaking of the clutch shaft not crank, my bad. going to check for the bearing between the 2 clutch push rods since whoever worked on the bike before was a bit of a hack in my unprofessional opinion. so anything is possible. That would not however explain the movement is the clutch shaft itself.

If i mentioned bearing i was talking about the one in the case not the pushrod from end play of the shaft point of view when the center nut is tight. No31 in the link. Or damage to retainer plate No10.
www.partzilla.com/catalog/yamaha/motorcy...973/ct3/transmission

the link below shows the end play i am talking about. seems excessive to me, what do you think?

Right--but with the clutch on & tightened, that end play should disappear as its all held against the big bearing in the case on the side you're on. Does seem excessive but there's no washer the other end as the last little gar on the end is pressed on. & everything is held over to your side. Best of luck.

So I must have something wrong in the assembly?
Tightening up the nut on the clutch shaft should take up that slack?