It's probably just the flu. This is a nasty one. My daughters was the same. 100-103.5. Up and down. She would sleep on me, and throw up with diarrehea...the works. Fevers are good to help fight off a virus or bacterial attack on the body. Our body heats up so our immune system can see the virus and attack it better plus the virus can't survive as well in the heat. It just sucks that they are so uncomfortable.
Watch her temp though. Babies should really go higher than 103 without concern. Don't feel the need to feed her if she's not hungry. Feed a fever is just a old wives tale. Juice and water when she wants it. Sips or tiny ice chips. Forcing food can make her body work harder on digesting and bowel issues than on fighting the cold. If the fever is too uncomfortable or reaches over 103, you can rotate motrin and tyenol. Tylenol every 4 hours, Motrin every 6. For this nastry strain of the flu, taking both Tylenol and Motrin is what kept my fever off. I had a 104.3 and I guess I was starting to say cooky things.
Also, if she can't keep her medication down, you may need to consider fever reducing suppositories...if that's how you spell it. I never got to that point but my doctor said vaseline and insert. Yikes but if it helps, right???
I wish you the best. It can be scary. Trust your instinct.