Katie, I don’t think your vomiting is due to pouchitis. There are nearly 22 feet of intestine between your stomach and your J-pouch. You could be having a medication reaction, or perhaps some upper GI problem (e.g. gastric outlet obstruction or other kinds of indigestion). I can’t tell exactly how long this has been going on, so I can’t tell if something like food poisoning or infectious gastroenteritis is a possibility.
I’ve never heard of using cefdinir for pouchitis, nor have I heard of every other day dosing (but recommended treatments do change sometimes). If you trust your regular doctor to know about pouchitis you might try calling to speak specifically with him/her rather than whoever is on call.