Acne can be very persistent. It is very frustrating. But ultimately this decision is up to you. You can try to get off The Regimen and see how your face does, but the fact that you are still getting breakouts while on it (although only once daily) tells me that your face is still acne prone. If you want to get the acne under control, the Regimen works best when done very strictly twice per day, every single day.
Also, keep in mind that for some people protein shakes may cause issues. http://www.acne.org/regimen-help.html#liftingweights
The products for the body are the same as for the face just in larger packages, plus the process for treating body acne is a bit different than the face regimen. But if you are asking if you can use the same cleanser, treatment, and AHA for face and body, yes you can. I would get the large sizes if you are doing both face and body (16oz).
Acne can be stubborn sometimes. For those stubborn areas, be really generous with the bp and use the AHA to spot treat as well. You could also try icing the area after washing but before applying any treatments.
Skin darkening in the beginning is almost always due to dry skin. Be sure you are using plenty of moisturizer and add some extra jojoba oil drops at each application. That should help. If it doesn't you may need to reduce the amount of bp you are using in this particular area.