Hi. I understand what you are going through. I am going through some autoimmune myself. I can tell you the cleaning up the diet, removing refined food, milk and as much chemical or refined crap as possible is helping.
The other thing that will help you is read Dr. Fuhrman books on fasting and eat to live. Also go to hacres.com they tell about autoimmune conditions being improved.
It is possible it is a healing crisis, but on the other hand maybe your body is dealing with more toxins or toxins are being processed. It is also possible the condition is being triggered by stress or worsening on its own. The good news is after reading Dr. Fuhrman's bood on fasting and have tried multiple small fasts, it has helped me with my skin issues. He says in his books most autoimmune conditions respond to method of fasting among other conditions.
I recommend you read his books and then try short fasts like 24 hr or 48 to see how you do as long as your doctor give you the okay. IF you are doing a long fast you may require supervision which Dr. Fuhrmand and Dr. Goldhammer offer. You absolutely must break the fast in the proper manner as it cause health complications and even death if done incorrectly.