When my legs decided to twinge in ways that made my lunges sad during stage one, I replaced them with step-ups-- the motion seemed similar enough that it would be a good substitution, though I'm not sure how true that actually is.

You could also try doing the static lunge, rear foot elevated thing with resting the top of your back foot on the step, rather than bending your toe, though I just started stage two today and tried that, and found that my balance wasn't very good that way.