Many people (including myself) experience a huge improvement to their skin in the first week, only to find they have a dreadful breakout in the 2nd/3rd week.
Dry, itchy and red skin are perfectly normal reactions while your skin is getting used to BP, but its important to moisturise and mosturise well and to also make sure you're starting slowly with the BP and not applying to much in the first couple of weeks. If you are finding some patches on your face are dryer and more irritated than others, perhaps apply less BP to those areas and apply more moisturiser. Its perfectly ok to apply more moisturiser throughout the day as you need it, so long as your hands are clean and you apply it with a feather light touch.
As for the moisturiser being brown, its hard to know if this is normal if we don't know what products you're using. Acne.org moisturiser is a yellow colour but definitely not brown.
After remaining clear for around 1.5 years following DKR (The Regimen), in March 2013 I decided to change to Epiduo. I use a pea size amount of epiduo each night, followed by a layer of topical antibiotic (Eryacne). I also apply Eryacne every morning and moisturise twice a day. After switching to Epiduo from the regimen I found that it took a good 3 months to get back to being perfectly clear again and now I might get one small pimple appear per month. I can live with that
I started following Dan's Regimen in September 2011 after suffering with acne for 20 years or so. I followed the Regimen instructions exactly and became 100% clear within 9-11 weeks. In December 2011 and after being consistently clear for over a month, I started to slowly reduce the amount of BP I used until I was only applying BP at night. My skin still remained clear however I sometimes switched to applying BP twice a day for a few days (perhaps once a month) if I felt a few under skin bumps starting to come up. I used acne.org products (including AHA and jojoba oil) and sometimes cetaphil moisturiser at night if I felt my skin was especially dry. In the gallery I show my week by week progress following the regimen.