Now in high school, you would never know that my daughter had any organizational difficulties. (Well, o.k., unless you open her closet.) She is a much happier person, understandably so, since now things aren't constantly going wrong for her. She is on medication, which I think was one factor in her improvement, but she is doing so well that the doctor thinks we can try going off of it this summer.
My suggestion to you is to keep trying things until your daughter is able to run her own show well. I have seen too many of our friends' extremely smart kids with organizational issues in middle school crash and burn in high school. Sometimes it is because they are self medicating and sometimes they are just sick of it all. Just because they can ace every test and keep up the grades while forgetting their homework regularly doesn't mean that it won't catch up to them. Some kids make it through high school only to fall apart in college. So it is good you are looking for answers now. I think it is easy for parents of really smart kids to ignore the problems, which you obviously aren't doing.
And about the celiac connection - I wonder if long term consumption of gluten in an individual having an autoimmune response to it causes some permanent brain changes. I also wonder if neural pathways that weren't developed at just the right stage can rebuild themselves over time, with help. It seems possible to me . . .