sounds like something could be wrong with the shift drum, or possibly a shift fork. you may want to pull the clutch cover off and take a look. Also on these Lt250r's be sure and use OEM headgaskets if you can. The lt i had was bad about headgaskets leaking. Use a torque wrench and properly torque the head to i believe 22ft lbs. may want to double check that.. I also used Ultra Gray silicone on the gasket surface to help it seal.
1995 Blaster. Bored .040" , midrange ported, head rechambered, pro series reeds, FMF fatty/Dg silencer, lightened flywheel, +4 timing, Hydro brakes, Lonestar +2 a-arms, Works dual rate G-series shocks, +2 swingarm,. More to come