Sorry to hear about your daughter...endometriosis can be such a difficult thing to deal with, but it sounds like other things are definitely going on with her. Does she have a history of heavy periods and have they checked her for anemia? Is she taking any hormonal treatments for the endo? Being so acidic and lacking minerals also means that she likely has an electrolyte embalance...I assume the naturopath put her on liquid minerals including trace minerals? When someone is highly acidic they are also very toxic. Anxiety can occur with both these conditions...and the medications will just add more toxins to her system.
Is she able to handle fresh juices without getting nauseous?...that would be a great way to alkalinize her body and the nutrients are more readily absorbed....also lots of fresh vegetable soups. Digestive enzymes may also help improve her absorption of nutrients. 40 herbs and supplements seems a bit excessive...especially if she can't metabolize them...what all is she taking?