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Please clarify, do you really mean the shift fork shaft, or are you trying to remove the shifter pawl shaft?
I'm glad someone finally asked cause to answer his question the way it is written would be "you have to remove the trap door to remove the shaft for the shift fork"...
You do not need to remove the trap door in order to remove the shaft for the shift forks, you only need to remove the outer right side transmission cover, top cover and shift drum. However... if you are attempting to remove the shifter pawl shaft, you must remove the gearset from the right side of transmission.