Hi Doug
I have been a long time lurker here, but as your problem is familiar to me I decided to jump in.
My engine is a 38 year old YSE 12.
I would suggest that your problem can be solved by resetting the linkages as suggested by Seanshine.
The manual is a little confusing so I will add my amended version plus a pic.
My engine ran out of fuel a few years ago and wouldn't start well, so I tried everything until I finally came across a comment on this blog.
The Yanmar YS engines...
He suggests resetting the linkages at intervals. I did that and it fires up first shot every time.
I still don' know why resetting fixed it!
View attachment 151115
Set the throttle to full power/open.
Loosen the connecting screw lock nut. (1)
Turn the connecting screw (2) until the punch mark is in the 12 o'clock position when looking down on it.
Only the connecting screw pin and no thread should protrude though the governor arm..
Loosen the regulator spindle lock nut (5) and lock bolt (6).
Lightly screw in the regulator spindle (4) until it seats.
Tighten the lock bolt (6) and lock nut (5)
Turn the connecting screw (2) counter clock-wise until the punch mark is in the 9 o'clock position when looking down on it.
Tighten the lock nut (1).
Add a small amount of grease to the connecting screw pin.
With fingers push lightly against mechanism. It should move freely against the spring pressure.
Start her up.
The Yanmar YS is noisy. It vibrates BUT it is the toughest little engine on the block.
I did a 200 mile trip down the east coast of Japan against wind and current all the way.
The yammy never missed a beat.
Best of luck and let us know how it works out
Gary