I did have back pain, but it wasn't horrendous, and coupled with the all-over pain, it didn't feel that significant.

What you describe sounds very similar to what happened to me though. I had had cystitis for about a week, started a course of antibiotics for it, but that evening I got really ill and feverish. I went to A&E and they took me in and put me on IV antibiotics. They said once it gets into your kidneys, oral ABs won't touch it.