I am sorry to hear about the flakes but am glad to hear about your progress otherwise. The flakiness was and sometimes still is not my favorite part of this regimen.
I read a lot of different posts on exfoliating with jojoba and it sounded like the best way to avoid/get rid of flakes was to gently and generously apply the jojoba oil to the face before the cleanser. I then let the oil set for several minutes and then gently massaged my skin. The best part was then using the cleanser to wash it off! Then I still added drops of jojoba to my moisturizer in both the morning and again at night. Even though my face had a ton of product with the full two pumps on moisturizer, I had more success by letting the moisturizer drop on my face than hurrying the process or using less. My flakes went down significantly by applying the jojoba this way.
Personally I might suggest not using the jojoba immediately before the BP to not interfere with the BP soaking into your skin. Did you gradually increase your BP each week or did you bump it up quickly? I actually had to decrease the amount of BP a tiny bit around week 4 due to irritation and was then on the full amount by the end of week 5.
Because AHA helps with exfoliation, it is a good product for skin texture and by default, the flakiness. On the Acne.org site, it says "Wait until your skin becomes accustomed to benzoyl peroxide. If you use it sooner than this it may sting badly." I waited until week 7 and I am really glad I did. My face was way too irritated to put additional products on before then. The flakiness died down by around week 6 for me and I don't even need the jojoba exfoliation before each cleansing anymore.
In a nutshell, I would not use the AHA until you can comfortably apply the entire dose of BP on your face (without applying the jojoba first). Instead, I would try experimenting with different ways to use jojoba to exfoliate current flakes and prevent future ones.
Again this is just my opinion based on my experience and I wish you the best.