Were both the spacers installed on the mainshaft and counter shaft before they were pressed into the bearing door?

 

Yes they were. When I rebuilt this tranny a few years back it had all new spacers bearings etc. I took this tranny out and put a new tranny in its own gearcase. This tranny I pulled the casette out of its case to get the case welded and the mainshaft and countershaft were never pulled from the bearing door. I simply reinstalled the casette back into the repaired gearcase and reinstalled the entire unit back into the bike. When I took this tranny out of the bike I had no issues with it. I'm starting to think it was a bad thing using the shifter forks in this tranny after they had run in the other tranny for so long. I gave them a good look and there is no obvious bend on the forks but when I check them with a ruler they appear not to be perfectly flat but not being someone who does line work everyday I can't say I have the trained eye to see a bent fork when I see one.

 

Here is something to check concerning the forks, with the top cover off put the bike in 3rd, grab each fork and give it a wiggle it should have a little play
if it doesn't then that fork may be bent and binding. Do the same thing in 4th.

 

Something else, in a couple of your pics, the 4th main looks really discolored as if it got hot. The teeth don't look very sharp on that gear either, if a single tooth gets distorted or you can grab a ridge or a valley in a single tooth with your finger nail it will make noise.

EDIT: I mean the 5th main.

 

Thanks Mark I went through all the motions you described.
Found the culprit when I was rolling the tranny around after putting in 3rd then forth and just happened to spot it.
Broken tooth was sitting in bottom of case

 

glad you found it

 

That sucks, but what caused it .?

 

Pretty sure what caused it was when I locked the tranny gears while installing the tranny and when I locked the gears to torque down the primary side the gears may not have been lined up properly, I do recall hearing a ping while torquing but wasn't sure what it was.

 

That'll do it.