Coeliac Disease :: 2 Years Into Being Gluten Free Still Sick

My daughter was diagnosed with coeliac disease end April 2014 and since then we have taken her completely off gluten.  She is now hyper-sensitive to even trace amounts of gluten and can be sick for days if she eats the tiniest of crumbs.  Her tests for gut damage were 300+ and she is down to around 18, but doctors would like her levels to be 7 or below.  We have been seeing a chiropractor and physiotherapist to help with her muscle spasms and aching over the last few years (back and legs).  She has been tested for lupus, rheumatoid arthritis, anaemia, vitamin D deficiency, thyroid problems, calcium deficiency and she came off lactose for a month.  Everything has come back negative - although in January this year the consultant put her on calcium supplements to be on the safe side.

However, she is in constant pain which gets worse by the evening (she rates most evenings as 7/10, 8/10 if she has a headache and saves 10/10 for how she remembers it feels when glutened) - her joints and muscles ache (no swelling).  She has to have her legs and back which are the worst affected parts, rubbed at bedtime and she goes to sleep with heat packs to ease the pain.  She gets a headache as a result of the neck pain about 1 a fortnight.  She can get very tired and last Friday she was sent home from school as she was tired, headachy and achy.  She came home and spent the day in bed.  She used to be so active and was able to swim 4 x a week in a squad - if anything she seems to be getting worse not better and cannot attend as much training.  It's horrible to watch her walking around like a little old lady at age 9.  In the last three months even during the day - her best day was 3/10 pain.  Naturally it really gets her down. 

I have been told that the gut in some people can take 2 and half to 3 years to recover - but surely malabsorption wouldn't make her feel worse?