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)
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)
- Nuts/Seeds? (Coconut?)
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!