The evaluation has been pretty comprehensive thus far. Other possibilies can include inflammatory bowel disease or irritable bowel disease.
The ultrasound and CT scan would indeed make the appendix or gallbladder/liver disease less likely.
An upper and lower endoscopy can be considered for a more thorough evaluation of the bowel tract.
These options can be discussed with your personal physician or in conjunction with a pediatric GI physician.
Followup with your personal physician is essential.
This answer is not intended as and does not substitute for medical advice - the information presented is for patient education only. Please see your personal physician for further evaluation of your individual case.
Kevin, M.D.
http://www.straightfromthedoc.com
Make sure you get the right tests for her:
TPO - thyroid antibodies - very important
TSH
Free T4 and Free T3 - actual thyroid hormones.