I had the same issue on my 99 KX250 and I hate to say it, but the fix was rather easy in my case. First, the original owner put a FMF pipe on it, and silencer. In my great wisdom I wanted to check the carb settings because it was bogging in 1st and screaming everywhere else. Long story short, putting the needle clip back to the stock position, made all my problems go away. 4th clip position (Stock) just got the bike back to quick throttle bottom end for me...Just something to check and easy to play with. FMF suggest 3rd clip setting and I even played with it up to the 2nd clip setting, but stock was the ticket.