I think you should start with the digestion. The rest may work itself out and is sometimes a side effect of poor stomach acid (not enough or too much, likely not enough in your case). Start with the digestive supplements and HCL and see where that takes you. Make sure you are taking in a good source of probiotics, including the two missing bacteria types, and the "bad" stuff will likely get sorted out as well. The gut is supposed to be pretty much self regulating. I don't think you need to worry about killing off bad bacteria that much.