The problem may be that your daughter still has a chronic infection that has eluded diagnosis. Eventually this may have evolved to an autoimmune situation. Since the autoimmune effects result in many of the observable signs/symptoms, the usual response is to place the patient on immune-suppressing drugs to control the symptoms. However, if she does have an undiagnosed chronic infection, this may do little in the long run to reverse the clinical condition, requiring the patient to stay on immune-suppressing drugs.
There have been other posts in this section on some possible alternatives to just using immune suppression to control symptoms.
Amoxicillin will only be useful against some of the pathogens I suggested might be causing the problem. If this doesn't work, then there are other Abx that may be more useful.
Thank you for your quick response. She was put on amoxicillin for 2 months for high strep antibody titers. I do not know what the current levels are right now.