I know that my Thomas was similar to your discription. He was generally pleasant during the days but when it came to eating or pooping we had issues. He always was extremely constipated and that was the reason he was started on Neutramigen in the first place. The doctor thought maybe the easily digested proteins would help his bowels. It really did not make too much of a difference for him although she said that most kids go 4-8 times a day on it. He was lucky if he went once and that was pumping him full of laxitives.
I do know that any type of starchy foods (rice, pototoes, squash, carrots) made him scream to high heaven and he began refusing to eat from a spoon at all. I finally settled on oats with sugar (natural laxitive) and pears. Those were the only 2 things that did not bother his belly at 6 months. My husband kept making fun of me and telling me he could not eat only pears forever. He is a great eater now!!!
I guess I would agree with Eden and Connor's mom - start to look at the relationship of all foods, poops and spit up. When are they happening more? How is it all related. Thomas pooped dark green for months and months and the pedi never cared about that. He was in excruciating pain all day because he would have to poop and then he wouldn't eat until he did and then he would eat too fast and then spit up and be hungry and miserable. He also could not sleep at night. he rested well through the day, but at night we would pray he would only start to get up at 1 or 2 beacuse once he was up, he was up all night. Sometimes he started at 10. It was horrible. To make a long story short, he was MSPI and we had no idea. He also had reflux most likely as a result of not being able to digest what he ate all day and night.
How does she eat? Squirmy throughout? THomas never lay still for a feeding and he latched on and off the entire time and then he would just fall asleep from boredom.
Try keeping a detailed food, sleep and poop diary for a week or 2 and see how things relate to each other. It may tell you a lot.
Jen