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Low compression.

According to smedspeed, the valve starts to open at 93 degrees BTDC, the cam holds the valve off its seat for nearly 45 degrees before it actually lifts more than 0.005.
 
You said you checked the timing and it was correct. If the cam chain has jumped some teeth, it wouldn't be, and you wouldn't be able to get it timed right.

The hole for the locating pin is in the cam not the advance unit. You need to remove the advance unit to see it .....

AdvancePinHole2.jpg


But, there is a way to discern the locating pin's location without removing the advance unit. Above the slot for the locating pin on the backside of the advance unit, there is a retention pin pressed into the plate, and it shows through on the front .....

Advance Pin Front.jpg


But there's a good chance the notched nut that holds the advance unit on will be covering it. Still, you can discern it's location. It's on the flat side of the unit, the side behind the direction arrow, just above the bent up tab. So, looking at the pic of your advance unit you posted, if it was taken with the motor at TDC, the cam timing looks good and I don't think the chain has jumped any teeth. Your "no start" issue is due to something else.
 
Ok, I obviously misunderstood, I thought you meant the hole in the advance backing plate.
The cam timing being out didn't didn't make sense as the valve timing appeared correct when I checked with a degree wheel.
 
Incidentally, smedspeeds valve timing disagrees with the Yamaha service manual apparently. Smedspeed says the valve only opens around .02 for around 45 degrees of crank rotation.
When I checked, I turned the crank anticlockwise until the valve lash was taken up, as it happened that was at around 90 degrees+-.BTDC. So by the time the valve opens any appreciable amount (say .05) the crank would be around 38/40 degrees BTDC, depending on the amount of valve lash.
 
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