I have been using the regimen for 6+ weeks. Acne has cleared, still small breakouts, but not as bad as before. My trouble is how dry and flaky my skin is. I can barely move my face. I am mixing in jojoba oil morning and evening and applying additional moisturizer throughout the day. Still no relief. I am ready to stop using the regimen despite the improved acne, I am extremely uncomfortable. Any recommendations?
A couple of things to try:
1) Try only using Dan's cleanser once a day and just rinsing your face with water (in the sink or the shower) for your other cleansing. Personally I've found Dan's cleanser to be very drying and cutting back to using only once a day really helped.
2) For flakes, try this in the shower: take a palmful of jojoba oil and "cleanse" your face. Then soak a washcloth and very gently wipe off the oil, being careful not to scrub. Try to only wipe in one direction, or wipe gently in little circles. Pat dry and see if this helped. This can help remove some of the larger flakes and hopefully help soften your skin. Do your regimen as normal. Repeat this oil method in a few days if needed.
Since you're past the 4-week mark, you can also try building in AHA+. This acts as a mild chemical peel for fading PIH but just a warning this will make the flaking worse before it gets better. But in the end, it will help slough off the dead layers of skin so that your BP can absorb even better.
Flaky, dry skin is not only one of the biggest complaints at this stage, but also one of the biggest reasons people give up. Just try and ride out this stage of the treatment the best you can. You'll get through it so hang in there! 
As someone who has been there and done that I know what you are going through. I was close to quitting as well around that stage because the whole regimen was very uncomfortable.
Have to considered switching to another moisturizer? At night I would use my Cetaphil moisturizing cream or lotion because it is very thick and really helps with the dryness and flakes. Also, throughout the day if my skin ever gets really annoying I would apply more moisturizer just to get a bit of relief.
As what DeLovely has said, AHA is made of awesome. This has helped my skin deal with the flakes. That mixed with jojoba oil and moisturizer has really helped my skin smoothen out and even the coloring of it.
Just remember that your skin is still getting used to the BP, with proper TLC, your skin will go back to normal. Promise!