I know this sounds retarded but is your air filter clean???
check your compression, pull your reads and check them out. I had a buddy rebuild his 250 r and couldnt get it to run right for the longest time and finally found a piece of piston stuck in his reeds. ran good since then...
are your carbs in sinc, (slides pulling equally)
clutch isnt slipping is it??
Just some Ideas that I have hope I can help...