If you're very low carb, try increasing your carb intake a little. (fruit, safe starches) The mucous membrane of your gut lining will be thanking you.

Also as Jen said, make sure to get enough fat.

Hypothyroidism may be also an issue. Get enough iodine and selenium (but make sure not to ingest any gluten in your case)

EDIT:

Ever did an elimination diet? Such bowel problems are often the result of food sensitivities and/or allergies.

Since you've cut out dairy and nightshades, try eliminating those guys: (and avoid cross contamination)

• Eggs?
• Nuts/Seeds? (Coconut?)
• FODMAPs?
• Salicylates/Histamine?

I had those problems with cheap olive oil (actually "extra virgin" but cheap). Then I found out that cheap olive oil is often diluted with soy oil. I'm allergic to soy.. hooray!

I am going to start with stating I AM NOT A DOCTOR! So you can take my response below with a grain of salt...(anyone know where that saying came from? Just some intellectual curiosity).

You list "thyroid" as part of a list of autoimmune disorders. Is it Hashimoto's Thyroiditis? 'Cuz this lovely disorder can swing back and forth between hyper and hypo (oh so much fun!) - which can cause you to experience bouts of tarry, diarrhea-like bowel movements (along with other symptoms). If you do have Hashimoto's, are you on a natural thyroid replacement (desiccated thyroid)? You may want to schedule an appointment with your endo to get your levels tested.

Also, you mention Celiac's, which I have (along with Hashimoto's Thyroiditis). I had to give up all fruit because it was causing similar symptoms in me (along with the tarry poos I also had stomach pains -- do you have stomach pains?). Have you had an upper GI recently? I found out from my latest endoscopy that I have gastritis (basically, my mucous membrane in my stomach is gone) and a peptic ulcer -- both damage from Celiac's that haven't healed (and get this, my Hashimoto's may have been caused by my Celiac's...gluten is evil!). In this case, you may want to schedule an appointment with your gastro to make sure your insides are...as well as they can be with multiple autoimmune disorders.

One thing I have learned from going Paleo with multiple autoimmune disorders is that you still need to work closely with your doctors to make sure your disorders stay in check. Which I have found they have...as long as I eat as close to the earth as possible (no processed foods...even gluten-free processed foods occasionally cause me issues). When I originally started following the "paleo movement", I was like "screw you guys, I'm outta here!" to my doctors...VERY BAD MISTAKE. I am still paying for it.

I am hoping none of the above pertains to you and it is just a simple elimination diet as Thomy suggests above...good luck to you!

I have had similar issues and history with bowels, thyroid, etc. I have discovered Siberian ginseng or eleuthero as helpful to the adrenal fatigue.

Eggs do this to me. I second the recommendation to try removing them and see if your symptoms improve.

I'm not a doctor either.
You know that your tummy issues are probably the result of immune disorder, strange that you had it as a kid as well. Is there gluten in your diet? Have you tried probiotics? The Paleo diet is supposed to be great for immune diseases.