Multiple Protein Intolerances Breastfed Baby

My daughter is 5 months old. Around 1 month she started with symptoms of silent reflux (couldn't lay flat, poor sleep, hiccups, grimacing when milk would come up). She was put on Pepcid for about 1 month when we ended up getting her posterior tongue, upper lip and cheek ties revised. This seemed to help for a few weeks and her sleep was a bit better, she could lay flat on the floor and take naps laying flat. We continued bodywork (craniosacral therapy) 3 months after revision. About Then, about 2 weeks after revision her sleep became extremely poor (and has continued to be poor over the last 2 months). Waking sometimes every 20-30 minutes at night, often agitated/thrashing when trying to sleep, very short naps. She seems to have some of the silent reflux symptoms back as well. Her stools became watery, mucousy and sometimes have red flecks of blood. The GI doctor says she has protein intolerance to something I'm eating. I've cut dairy, gluten and soy several weeks ago, and have trialled several other common allergens with no relief. I've recently tried Kali phos and coffea cruda for her poor sleep and Nat Phos 6x for the reflux issues. I'm wondering what remedy might be helpful for agitation/restlessness and better sleep. She wakes often and wants to nurse because I think it's the only thing that soothes her inflamed gut. She won't nap unless I'm holding her and it's usually short lived. We both need better quality sleep and I'd love for her tummy to feel better while I continue trying to pinpoint what's bothering her!