The BP step rarely ever disturbed my skin, even as I was just starting out. Through trial and error, I found that the thing that always kills me is the moisturizing step. Even gentle oils and ointments that are meant to soothe skin like Aquaphor have this effect. Anything emollient on top of BP makes my skin go insane and irritates it to the point that I get welts. The only moisturizers I can tolerate are super mattifying formulas that don't linger. Now, after having used BP for a few months, I don't use anything over it. I find that moisturizing is a useless step, but then again I have extremely oily skin. I deal with the flakes by exfoliating in the shower everyday or every other day. Clarisonic is great and scrubs have been helpful. On the days when you're too sensitive, just run your fingers across your face after your skin has gotten sufficiently damp and gently rub off all the dead skin. I bring a mirror in the shower with me and do this regularly, as tedious and time-consuming as it may be.
Experiment on your own, as The Regimen and Dan's advice may not work for you. Everyone's skin is different. I've struggled with BP for so long because the golden rule is that you have to moisturize like crazy after. Well, for me it was the moisturizing step that always destroyed my skin and kept me going back to the drawing board. I feel like many users who haven't done well on The Regimen have reacted similar to me and never figured out how to hack it for their own good.