The only time I would adjust the stop bolt would be after all the other adjustments are complete. I would start with the pedal freeplay/lever to throwout bearing spacing. If set correctly(around .1" between lever and bearing face with pedal all the way up), this should result in about 1.5" of pedal freetravel and the main gearbox clutch being fully disengaged when the pedal reaches about 1/2 way down. Next comes the PTO clutch adjustment. With the clutch pedal held at the point where the main clutch disc is free/fully decoupled(1/2 way down), the PTO clutch nuts should be adjusted to just start to lift the PTO pressure plate at this point. A little operational trial may be needed to refine this relationship. The end travel stop is then adjusted as Quicksand describes so that the pedal can only lift the PTO pressure plate just far enough to fully release the PTO disc as it reaches the endstop. Setup this way, full pedal allows you to shift the PTO, and half pedal allows you to shift the gearbox without effecting the PTO engagement