Did the doctor make a scotch tape test? There is a parasite which is really common in children, called pinworm. The worms are active at night, feed of sugars and starches, and move through the intestine during the month. The pain from pinworms is like a needle beside or above the belly button. This comes when the females bite into the gut wall of the lower part of the small intestine to mate. They then wander down to the colon, lay eggs around the anus. The eggs can be inhaled, which leads to a nasty, ongoing cough, since the larvaes try to get into the stomach again. Common symptoms are: nightsweats, nightmares, weakness, itchy bottom, nausea and vomiting, bloating, pain which gets worse during the day, sometimes anemia (they hinder the uptake of b12) and weight loss.
Pinworms cannot be tested with the usual stool sample! (95% false negative). Good luck!
No she has not had those two. I would think it would be stress related but she is woken up from it like clock work. After a day of searching, Cyclic Vomiting Syndrome seems to fit. I am having her set up with a GI specialist right now.
You don't mention an endoscopy or colonoscopy and I feel she needs to have these tests as well so they can actually view her stomach and colon. If they find nothing on these two tests you may want to have her see a child psychologist to rule out anxiety. I hope this helps, I know how worried you must be and frustrated!