Yes, the vertical shaft is the pump spindle. If you rotate the shaft at around 500 rpm or so with a drill (in the normal drilling direction, clockwise when viewed from above), and keep reversing the direction of the transmission, while watching the oil in the filler neck, you should get this sorted out easily. Do not reverse the drill, of course: just switch the transmission between forward and reverse. Aerated oil looks foamy-white. When you get all the air out the oil should look just as clear as when it's in the can. Remember, the oil has to be continuously clear: the odd clear patch does not mean all the air is out.
