With the shift rod pivot pin removed, it's very possible that the shift yoke may have fallen off.
If you pull up on the shift rod, or move the throttle in a manner that moves the shift rod up, if the pivot pin is removed it's possible that the shift fork may have moved upwards to the point where it disengages from the two pins on each side of the yoke. If this happens, the yoke can rotate 180? and fall off the shift pin.
The shift yoke is kind of horseshoe shaped (see pictures in attached link in post #36 above). If the opening is pointed down, and the shift fork is engaged (which prevents if from spinning around), it will stay on the shift pin. If the opening is pointed up, it will fall off the shift pin even if the shift fork is engaged with the pins.