We went and saw Chels's Rheumatologist today and it seems, all is well. While her blood work is showing her to be relatively normal (if you know 13 year olds you understand this statement to be only somewhat true) we do have to start keeping a journal of her symptom, when they occur and if there is anything she does or does not do that helps.
The doctor seems to think Chels contracted a virus, which in turn caused her immune system to go haywire because it is already compromised from her Hashimoto's Thyroiditis. I am glad she is feeling better. Chels is still having some minor swelling and stiffness in her hands when she wakes, but compared to what she was going through, this is great news. Oh, I almost forgot the pain she has been having around her kidney area. Well, we thought it was her kidney area; even the pediatrician thought this. Apparently pleurisy causes the same symptoms that Chels has been having and this would make since as it kept going from the right lung to the left lung area. If you are not familiar with the term pleurisy, this is a condition in which the pleural lining of the lungs becomes inflamed; which seems to be common in people who have these immune responses.
Thanks to everyone for the well wishes and hopefully after a few visits (she has to return every three months for a while) we won't have to deal with the issue any longer.