We try our best to make sure when disassembling an engine we bag, tag and keep track of all the parts.  So I had everything except a 1/4" ball bearing that I knew went into the clutch rod space.  Could not find that bearing in all my stuff.  Got a new one and moved on.  
So I get the tranny installed and all is goos in neutral and put the two halves together.  Added what was needed to then test if I have the clutch shift adjustment correct and the darn thing would not shift.
I made a call to Dale Sweger and neither of us could figure it out so I split the case again and the sealer was still fresh.  I pulled the detent plug and it would shift - so what was up with the detent plug?  I had the spring and ball bearing installed and it was locking up the shift 
Sooooo   I pull the plug, pull the spring and look inside the hollow plug and sure enough there is another ball bearing (the correct one for the plug and the other 1/4" bearing that I was missing was being added to the plug making it too tight.  So I found the 1/4" ball bearing and now know the detent bearing is larger.  Lesson learned for a first time re-builder but a good out come as now it shifts.  

Glad you got it sorted.

For anyone that is interested and didn't already know, the size of any ball bearing can be "read" from the part number. Shown as a fraction of an inch, it is the last digit of the first block of five digits in the part number, over the first two digits of the second block of five, so in this case 5/16.

BALL for Yamaha - order at CMSNL
 

GR8 wow that is some kind of coded sorcery there!