I am looking over the kickstarter. Please see if this amount of pre-load on the spring looks correct. I have noted the service manual states to note the preload on disassembly. Of course, I skipped that step.    BUT, I took a picture during disassembly.  From what I can tell, is about 225 degrees preload or a 1/2 turn plus about 45 degrees. Does this look good?  I don't want it wound too tight or not recoiling enough.

This pic taken during disassembly.

The spring sits preloaded behind a tab down the other end from where i'm looking.
Thats if the tab is there & not broken off.
I'm going by memory when new so could be corrected with more recent experience.
So when you engage the shaft you then turn it a little to find the kick assembly stop in the case which effectively gives it a bit more preload.
Then it never returns to the tab as the kick stop prevents that.
So through its kick cycle it just winds up more, then comes back to the case stop.
So the tab is safe untill next dismantle & assembly.
I'm guessing if the tab gets flattened somehow then you'd need to tweek it out for the spring to get behind it next time.
Also guessing if the tab broke off all it would mean is you'd need to start winding the spring from further back to end up with same result when shaft is home on the stop.
Shaft can only go in right or half a turn out. If the stop is on the shaft with shaft & stop dots aligned then can't go wrong.
Hope i've not overly confused things. Best of luck.
Also i'm sure you're onto it but i see the half circles falling out with washer moved off. Don't panic.

Revisiting previously mentioned shim. The lateral clearance on the main axle is ~1.75mm without the clutch bolted on.
According to the service manual, allowed clearance is 0.5mm. After adding the 1.5mm shim, I'm down to < 0.5mm. Service manual states that if clearance is beyond 0.5mm, change shim thickness. I can't find anywhere else this shim would be used.(*yet). If the shim fits, you gotta commit?

Ok, a little progress. All spins freely.  Next up, add piston, cylinder and setup the VAPE ignition timing.  As I recall 2.9 degrees BTDC.
 

That's good progress.
I'm sure you mean 2.9mm not degrees.
Don'[t panic, 'typo' i'm sure you know what you mean.
So no washer on the main shaft?,
i realise the parts thing doesn't show one between circlip #10 & bearing #11
www.partzilla.com/catalog/yamaha/motorcy.../dt360a/transmission

I left the shim in. The final test will be after it is heated up and tested. I used your install the crank in left side first method and seemed to work well. 

update: main axle clearance = 0.3 mm with 1.5mm shim added.

Added cylinder today. I thought Yamaha had brushed the left side of head from factory, but after looking at this pic from Yamaha global, I guess not. May repaint that little spot satin black also.
global.yamaha-motor.com/showroom/library...l.php?id=AP000197348



 

Added VAPE Ignition today. A few comments for those interested.

1. Put plate on by centering bolts in slots. There are 3 bolts provided w/the kit to secure the plate to the case that are 20mm. They are too long for the DT360A case. I bought three 16mm bolts that worked perfectly. They were M6x1.0x16mm.

2. Setup dial guage, find, TDC, then turn engine clockwise to 2.9 mm BTDC. Go a bit past this point (I use 0.5mm past), then turn counter-clockwise back to 2.9mm BTDC. This takes the slack out of the clearances. Note, dial gauge will spin counter-clockwise, so be sure to stop on 0.10mm (using RED numbers on gauge in my case).

The instructs are on page 17 of the service manual on this site. Warning: The DT250 is a few pages before. The timing is different for it.

Gauge Info:
Full sweep = 1mm
major increments are 10,20,30,  ( 0.10, 20, .30mm, etc)
minor increments = 0.01mm
As displayed gauge = 0.10mm

3. Add flywheel, aligning to arrows on plate. It was a close fit, but would recommend at least 1 of the 4 thin washers provided by VAPE for nut clearance. Snug down the flywheel.

4. Go back to TDC and re-check your work. Adjust plate behind flywheel as needed for alignment. TIP: use a small screwdriver between the bolt in the slot and the slot to twist and finely adjust plate. Tighten/Torque all as required.
A T-Handle hex wrench will come in handy.

Will follow up with wiring as soon as I bolt the engine on.

Good progress. Wish i could afford a Vape system, they look a nice setup.
By the looks there's room to alter the plate with flywheel tightend up & ready to go, which would be a bonus.

Yes, plenty room to adjust plate after flywheel in place. I sure hope it works well for the cost. What I really want to see is how stable the lights are at night.