Fitness Programs Question

I'm working on my Adirondack 46 (24 into it) and used your 12 week program to prepare for a lengthily, multi-peak traverse. As I completed it with plenty of gas in the tank I can say the program worked for me. However, I have a couple of questions (to see if I'm doing it right).

On the step-up, side-step, step-downs...when, for example, a set is supposed to be 40. Is that 1 rep when both legs have made a step? (i.e. right...left...ONE. right...left...TWO)

Same for Mountain Climbers. Is it right...left...ONE right...left...TWO. etc etc?

That's how I was doing them, but MAN that makes for a long workout, especially when combined with an hour+ of cardio.