I know that on my MT250 when I got it running the clutch was stuck. Im not sure if this is what you mean, or was part of your problem. It sounds to me like a clutch or shift fork problem. I started by taking the engine case off and taking the clutch apart and soaking it in fresh oil. Also it sounds like it is part of the gears you can try putting a little seafoam in the oil and running it like that for a little bit and then draining the oil, and changing it, but I dont know that any of this will do the trick, because it also sounds to me like it could be bent shift forks, but maybe someone wiser can add to this.