You're right to go back and ask questions and push for answers if you're not comfortable, but also be willing to give your docs some credit. While most stomach viruses run their course very quickly, some do go on for weeks. One of my brothers was out of school for 3 weeks as a kid with a mystery stomach problem (occasional vomiting, diarrhea, cramping, pain, loss of appetite). My mom is a nurse so she's seen a lot but this confounded her and the doctors. Then it went away as suddenly as it came. I had a similar bout of stomach weirdness that lasted a few weeks in high school. Miserably uncomfortable for several weeks, at home unable to eat or sleep due to pain, then all better. Had a bunch of tests that came back fine and never learned what it was.
I agree with the idea of keeping his head elevated when he sleeps. The night vomiting might be from pressure and reflux at this point and will hopefully go away when the virus is gone and his belly is back to normal.