Hi there. I don't really have a concrete answer for you but my first thought with her having a fever is that she is thirsty at night and therefore waking up. When Molly is teething at night (which seems never ending and still NO TEETH yet!!) she often wakes up and her cheeks are just burning hot. I will give her water which she gulps down like she is dying of thirst, then will go right back to sleep. She often does this a few times in the night, all times drinking like there is no tomorrow!!
Just my thoughts, hope you find a solution!!