Thanks for writing in with your question. It sounds like you are doing wonderfully with your program. Wow, you are running a full time program! How exciting!
It's really great that you are seeing the DAN Doctor because they can advise you on how to use diet, supplements, etc to help your son with his Bio-Medical system. Often when our children stimulate their genitals repetitiously, they can have internal issues (such as yeast overgrowth) which can cause them discomfort, or itchiness and they are taking care of themselves when they do this.
You can see it as an ism (a repetitious and exclusive behavior). When he starts to do this behavior, first try offering him some sensory stimulation on his body (he is obviously seeking some input), offer him squeezes on his head, feet or hands. If he responds, great! You can continue doing that as a way to help his sensory processing sysetm get the input it needs and also create more interaction around it. If he does not respond and wants to continue stimulating himself then move away and do something repetitious as a way to join him, perhaps you could tap your feet to the same rhythm or rock back and forth on your feet until he is finished.
As he does this, you want to remain comfortable, loving and accepting and know he is doing the best he can and it's nothing to worry about. I would also incorporate lots of sensory stimulation into your play each day (e.g. rides, rubs, scratches, roll on the yoga ball, jump on the trampoline, etc). We have seen many children be able to manage and regulate their sensory processing systems so much more easily once they are consistently doing more time in the playroom. So you are on the right track. Keep going, we are cheering you all on!