I would also guess she is bleeding from somewhere, probably in the small bowel. That is essentially what the hematologist told us when we went - that the only way my daughter's Ferritin could have gotten so low is if she was bleeding from somewhere.
Our hematologist and GI would also do a blood transfusion if hemoglobin was 7. The hematologist said under 8 and he would do one ASAP. But they do need to figure out the cause of the bleeding.
I really think you need a second opinion - have you called CHOP and BCH or Cincinnati Children's and seen if they will do record reviews? In that case they would review her scopes, her pillcam and everything else. Like MLP said, they can be covered by insurance, and if it is just a record review, you won't have to travel.
They usually have someone who handles second opinions and coordinates them. Just call and ask - my little penguin gave you good advice above. They really do a lot of second opinions and are used to coordinating.