Hi and welcome. Hoo boy, I'd cry if I ever had to take prednisone. I don't doubt that it's a lifesaver, but the side effects. It turned my dad into someone I barely recognized, luckily he could come off it.

Atkins 72 sounds like a really good plan for autoimmune issues. Have you explored the AI specific recommendations for LC eating? I'm thinking of clinicians like Dr Perlmutter, Dr Wahls, and some of the carnivore crew. I can't find the recent threads at the moment, and I'm probably forgetting some of the obvious ones, but the general consensus seems to be that there are a lot of foods that healthy LCers can get away with that will cause trouble for people with AI issues - gluten, casein (dairy), seed oils, legumes, solanaciae vegetables (tomatoes, peppers, eggplant ), oxalates (certain leafy greens), nuts, eggs, chicken, breathing air ( j/k) ... not necessarily all of the above for everyone. An elimination diet followed by slowly testing out one food at a time has been helpful to many. All the label-reading can be a pain at first, but like that quote in my sig, it's only effort until it's routine. You memorize what you can and can't have.

Best of luck, keep us posted.