Oh bless her & I am so sorry you are going through this 
On the plus side you now know it is a strong possibility, it took me 13 years to finally realise that & my DD ended up in a wheelchair, B12 injections had her walking again, sleeping again, SPD much improved & anxiety hugely better too, in under 2 weeks.
She looked skeletal/ghost like too, anxiety, spd & gastric trouble were early signs for her too, but it got worse over the years after she had various drugs & treatments that deplete B12, such as certain antibiotics & gas used for dental work.
Iron deficiency anaemia can actually be a symptom of B12 deficiency & Vit D deficiency often seems to go hand in hand with it (my DD & I both had that too)
B12 & Folate aren't standard tests, so too often aren't checked. They can also go hand in hand too & have similar symptoms.
You need to ask your GP if these tests (B12 & Folate) & her homocysteine have been checked. Homocysteine is the level of toxins that build up in her system if she doesn't have enough B12 to mop it up. If these tests have been done, you need to get a print out of her results. If the haven't been done, insist that these tests are done as a matter of urgency.
Too often Drs don't understand B12 & related results, kids need more B12 than adults, plus the tests are recognised by NICE as unreliable & so deficiency often gets missed.
Also look at her Eosophils (sorry that might be mispelt) this is a parasite marker, if there is no other obvious reason why she might have B12 deficiency, then a parasite could be to blame & are often missed.
In the link I have added below, on the links page you will see "Pat Kormics B12 Facebook Support Group" please join this group. It was thanks to them that I gained the knowledge to not only realise my DD has Pernicious Anaemia, but to educate her doctors & fight treatment for her
Treatment has been life changing, it has even improved her Ehlers Danlos Hypermobility symptoms, which again seems to be linked. Her allergies have gone, her pain is 90% improved & so much more.
The group can also help you with understanding how best to treat Vit D deficiency, NHS protocol unfortunately isn't great. Natural Vit D is far better than the prescription stuff & it needs to be taken with Vit K, Magnesium & fat to work. I switched our treatment to this & the difference was amazing. Bone pain is a big symptom of Vit D deficiency & it stopped completely with a change of Vit D treatment. My dad has recently seen big improvements with natural Vit D too. You need to do this with your doctors help though, they need to be rechecking her Vit D to see the improvements as too much can be bad for her too.
I really hope this helps