Big giant hugs to you, i have been there is it SO hard. Sleep and potty stuff are so hard with these kids and "experts" like OT are so reluctant to try to help with them (maybe they just have no idea either). Even though it is miserable your daughter is on the right track in a way, she is neurologically very disorganized and lots of touch and close parental presence is what tends to organize babies neuro system - it's just that she needs so much more and she still only has two parents! What would happen if you let her sleep next to you to begin with so that she could be reassured by your touch before she fully awakened and became upset and anxious? (I know this is a shift in paradigm but co-sleeping is very popular among certain groups and a common need for our special needs kiddos) Would she let you wear her in an Ergo or Mei Tai carrier for a few hours during different parts of the day while walking, shopping, doing housework ect so she can have that kangaroo care that she is seeming to want during the day too? What else does she find calming?

Absolutely explore the food sensitivities too. Casein free gluten free is very popular and there is a newer one called GAPS that is very focused on healing so you won't always have to be on a special diet. We are currently transitioning from CFGF to GAPS and so far I've been very impressed.