"I don't understand this "in gear clockwise" and "in neutral counter clockwise" stuff. "
Sorry about the confusion, What I meant is that like you said, in neutral I was able to rotate the crankshaft nut counter-clockwise. When I put it in 2'nd gear it was a little harder to rotate it counter-clockwise (may be because it was in gear) and since I was using my computer to record the piston movement, I was using one hand and so I rotated it clockwise and it was easier to do so. I was sitting facing the primary chain.
I agree, this is really puzzling, I am going to open up the gearbox outer cover and check to make sure things are in order.