Everyones experience with the acne.org regimen differ in many ways, some get completely clear skin in the first few weeks of using the regimen whilst others see an improvement after several months, some don't experience any flaking whilst some have extremely flakey skin for the first few months followed by smooth skin. Not to mention a number of other variables that can hinder ones success on the regimen. I too am on the regimen (this being my second round at it, and the two experiences are slightly different). I found that my skin showed great signs of improvement the first week, followed by a breakout and then those healed up pretty quickly, but began to get a few more breakouts on the 5th week in. I would say it is pretty common to have more breakouts in the beginning stages of the regimen (such as yourself) but give it time and things will improve (patients and consistency is key to achieving clear skin). Remember pimples that you physically see have been lurking under the skin for a few weeks before you are aware of them, so these are just coming to the surface now.

You mentioned darkening of the skin, this again is a normal occurrence with the use of benzoyl peroxide (and this too has happened to me) but this soon goes away, especially with the introduction of the acne.org AHA (which you can now start implementing into your routine as you've been on the regimen for a month). This helps sloth off the essentially dead skin thats sitting on the surface of your skin giving it a darkened effect.

I managed to achieve completely clear skin the first time round in 2-3 months of starting the regimen. If I were you I would stick with it for at least 3 months total and follow Dan's instructions to the letter, and avoid adding any further products into your routine other than a good sunscreen (spf 15 or higher), if there is no improvement by then, than perhaps stop. Best of luck with your journey to clear skin.