The crank is installed in the left case half. With the transmission installed in the right side case half should I remove crank from left side and reinstall it on the right side along with the transmission?
I think it would be okay to leave the crank in the left side and transmission in the right as long as I get the shift fork shafts aligned and seated accurately when pulling the cases together.
Thanks for any input.


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I dont have time now sorry, off to cut firewood, but if it were me & seeing you have the crank pulled into the left i'd shovel the trans into the left case then the right case will slide on over the crank because right side is a slide fit held tight by the crank nut. When you tighten the nut i give the crank a good tap on the mag end to destress it as the nut will be trying to pull the crank over to the right bearing. Only talking next to nothing it will need to move over but it makes the difference. You'll find that if you turn it after tightening the nut the crank will resist slightly. One good tap with a Copper Hammer will free it & set it. Don't forget the crank shim on the right!! Ok that's about all I wanted to say anyway. Have a happy day.
 

Greetings from Tennessee. 

Thanks for the information. That’s what I’ll do. Sounds like a much better way to go. I appreciate the details & the hammer tap advice.
Regards

Copper, brass or lead hammer only..... the crank threads will thank you
-- Ray

Only have plastic or rubber. I can buy a copper or brass if the plastic won’t provide enough shock to reset the crank.
Bang the mag side of the crank after primary drive gear and concave washer installed,  correct? 

Just sit a block of wood against it the hit the wood with another block of wood could be enough. Might need nothing, just turn it & see how it feels after tightening. The washer i mentioned was on the crank on the right side before case goes on just so we're clear on that. I realise ya talking concave behind the nut though. All good.
www.partzilla.com/catalog/yamaha/motorcy...973/rt3/crank-piston
Number 12. 25-44-0.3mm or 12 thou thick in round figures.

Cases went together smoothly.
Assembled gear shifter shaft and the little spring operated actuator that is supposed to grab the pins on the shift drum. The hooks on the actuator are not aligned properly with the shift drum and will not engage with the shift pins. Neutral stopper is installed and aligned correctly. When I manually rotated the gears before reassembling the cases, the gears shifted smoothly. 
Obviously I’ve gotten something wrong here.
I took a short video I’ll try to upload.
Any thoughts are appreciated.

look forward to the video thanks.

You'll need to upload video to YouTube or Vimeo and post link here.

(For the time being, photos will also need to be hosted on 3rd party site and linked here)