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.
I would not use any other acne medications without checking with your dermatologist first.
Your doctor will need to get an accurate gauge of how Accutane is working for you in order to know when dosage adjustments may be needed. If you are using other medications that he doesn't know about, he may not get an accurate picture of what Accutane is doing.
Also, using other acne medications while on Accutane will increase your chance of dry skin and irritation. Ideally you don't want to create more irritation as Accutane can be extremely drying and may be irritating at too.
Bottom line, don't use anything that your doctor isn't aware of.
My best advice is to just make it part of your usual morning routine, rather that "add in extra time to do it".
For instance, most people shower or wash their face in the morning anyway so that really is not an extra thing to have to do. After you have washed, go ahead and get your clothes on. By the time you are dressed your face should be dry enough to apply the bp. Take a couple of minutes to apply the bp then as it is drying go about your morning. Fix a cup of coffee, eat breakfast, fix your hair, feed the dog, check email, pack your backpack or whatever you would normally do to get ready to go. Then apply the moisturizer and you are good to go. It really should not add a lot of time to your morning unless you are just sitting around waiting in between the steps.
I don't honestly have any tips for these areas. Mine are always lighter too but since I'm a blonde, it just looks like highlights in my hair and I use a brow pencil on my brows to make them a bit darker.
Rather than jump in with the full amount, go ahead and start as a newcomer would but you can probably go quicker in advancing the amount up. Whereas someone new to bp would take a month to work up to the full suggested amount, you can probably get there in a couple of weeks.
Unless you have some super powerful fan, having a personal size fan blowing on your face shouldn't be irritating and will help the skin dry quicker.
One other tip, after you have washed or showered try to apply the bp in another room where there won't be so much humidity. And yes, as control panel replied, be sure your face is completely dry before you apply the bp. It won't absorb well on damp skin.
The Acne.org Regimen usually works quite well for most cases of acne without the need to add in other stuff. Here are Dan's thoughts regarding adding salicylic acid. http://www.acne.org/regimen-help.html#salicylicacid