Dont take me the wrong way. But it sounds like you didnt break it in the way the owners manual says that will definetly cause premature engine wear and could have been the culprit to your problem. When you get it back from the shop be sure to break it back in the way they tell you to.
400EX- Renthal Bars,MotionPro Twist Throttle,Pro Design Kill Switch,AC Mudscreen Frt Bmpr,AC Fullbody Skid,AC Swingarm Skid,AC Pro-Peg Nerf Bars,Steel braided brake lines,Denton steering stabilizer,Raptor EZ-Pull Cluth Lever,Maier Universal XC Handguards,White bros. E-series Pro-Meg Exhaust,K&N Air Filter w/outerwear,Works Shocks w/Shockwears,Wiseco 440 kit, Hotcam,Eichner series Edlbrock carb,Hinson clutch and basket,6 degree timing key,FST oilcooler,Oversized oil tank