In my very limited experiance, I own 2 YS motors, 63 FZ and 120 SC, and both of them exhibited similar kinds of issues when brand new. Surging, poor running and stopping, just like you expieranced. However, the more running they had, the better they became. I did have to change glow plugs early on as new engins tend to eat plugs.. But now they are properly run in, I don't change any settings at all, no matter what the conditions. Just fill up and fly.. Easiest engines to operate I've ever owned. I think new engins just need a bit of fuel through them to settle down.
I used Troy Newmans set up method to tune them initially,
http://www.patternflyer.com/troy/?page_id=13 which gets you in the ball park, and then very fine adjustments untill they run like a swiss watch. Easy. Like David, I think alot of people are ham fisted with tuning and get frustrated, especially when the engin is new and still setteling down. Just have patience and adjust cautiously..The grunt these YSs' can produce is worth it.
Roger