As long as you take the entire protocol as directed, I wouldn't worry about the negative effects of the berberine/barberry/goldenseal, b/c you are taking lactobacillus sporogenes which are hardier and stronger than your every day acidophilus type bacteria which are not affected by those ingredients. You take the lactobacillus sporogenes for the duration of the protocol. I don't believe that quiet digestion is going to address acid reflux, but if I were you, I would call him for a free consult Tuesdays (check out his website for details, it's first come, first serve) and ask him about reflux. From what I have heard from him/researched it's an indication that you are overproducing/underproducing acid (symptoms are almost identical) and you need to correct that. Regardless of whether or not you have candida, the reflux seems to be a separate issue, though often aggravated or exacerbated by candida.
As for vitamin D, I take 10,000 IU, but am only going to continue that dosage until I finish the protocol. I also live in southern california and will start surfing again next week, so my vitamin D requirements/needs are going to go WAY down if I am baking on my surf board for multiple days on end.
Hope that helps!