I pulled the oil drain plug with the magnetic chip detector..... found a few small slivers of metal (And I've only logged 18 miles since transmission swap), so I decided to pull the motor back out and see what's going on.
It's on the bench now.
When I put all the transmission shafts in the lower case half and put it in neutral, it makes no noise if the case is level.
If I tilt the Clutch side of the case up (simulating the bike being on the side stand) the first gear wheel (Item 21 in the transmission parts list) has just enough freedom to barely touch the dogs on the fourth gear wheel (item 20 in the transmission parts list). Both of these gears are on the drive axle (item 12 in the transmission parts list).
The looseness of the first gear wheel relative to the drive axle initially bothered me.....
Then I compared the fit of the first gear wheel in my original transmission (which had the skipping second gear syndrome, but absolutely no clunking going on.) That first gear wheel fits very much the same.
So, I put the old transmission shafts back in the case.
After I removed my middle gear from the original transmission, I did not install the other middle gear/damper spring/cam ect. from the other transmission onto the old shaft.
As such, I am able to slide the drive axle left and right in the case.
If I slide the shaft to the right, I can minimize the freedom allowed to the first gear wheel.
In that position, I get no clunking between the first gear wheel and fourth wheel dogs.
If I slide the shaft 0.05 to the left, I get exactly the same clunking noise caused by contact between first and fourth.
When I swapped the middle drive pinion off of the original transmission, I measured the thickness of the washer under the two halves of the infamous split washers (Items 5 and 6 respectively in the middle drive gear parts list). I found one measured 0.015 thicker than the other. The parts list just list this as a washer... not a shim.... there are no different thicknesses offered in the list. I see nothing in the manual that addresses shimming the shaft position relative to the transmission position in the case.
When the split washers wear (causing the classic second gear failure), the damper spring takes all the slack out by moving the shaft to the right which progressively diminishes second gear dog engagement as the washer wear more and more.
Based on this, I surmised that I would be better off to use the thicker washer which I assumed buy me an additional 0.015 inch engagement in the second gear dogs.
I believe my noise is the result of too much play between first gear wheel and the shaft.
Further, I believe I made this play on the shaft worse with my selection of the thicker washer.
Tomorrow, I will swap the thick washer under the split washer for the thin one I did not use.
Hopefully, this will tighten the first gear wheel up and my noise will go away.
If not, I believe I can decrease the thickness of that washer until my problem does go away.
I do not think changing that washer thickness will have any effect on the middle gear set lash as that is controlled through separate shims.
Would really like to hear opinions before I proceed...... my help is growing weary of removing and installing the motor from this beast!!!