I have dealt with UTI's, kidney infections and bowel problems with my daughter since she was a baby. She's 12 now and still deals with it. She's had many high fevers with few easily recognizable symptoms. We've mistaken her infections in the past for stomach viruses and other illesses that were going around when she was very young. As she got older and into school, we still had some trouble recognizing her illess as a UTI or kidney infection. She never complained of pain in her back or side. She never complained of pain when urinating, or any other symptom usually associated with a UTI or kidney infection. She would usually have a headache, nausea (sometimes with, sometimes without vomiting) and a high fever anywhere between 103 and 107 (which was extremely frightening, by the way!). She usually wouldn't eat or drink unless I made her try.
It wasn't until she was 5 and put in the hospital that we discovered she had kidney reflux. We began seeing a urologist regularly and she was put on a preventative antibiotic. We were told she'd have to stay on that until she grew out of the reflux (which involved getting the VCUG test every year), but she had developed a diverticulum and needed to continue the antibiotic even after the reflux was gone. She's been off of it for a couple years now, but she still gets at least one infection a year.
Over the years, we've learned to question every symptom as being more than it appears. One week-long stay in Kosair Children's Hospital was more than enough! We learned how to handle the high fevers, have used many home UTI tests (even though her dr. doesn't accept the results), and make sure she gets started on an antibiotic right away. There were a few times I remember having to get a different antibiotic (usually an injection the second time around) because she wasn't getting better. We saw the 105-107 temps when the infection had moved into her kidney.
I hope that helps a little, and I hope your little one gets better soon. I hope she's not one who will be prone to infections like my daughter. I know how awful it is. Our thoughts and prayers are with you!