What Causes Pain While Urinating And Back Pain Post Unprotected Sex?

A week ago my fiancee and I had protected sex, but the condom broke prior to ejaculation. We continued however she told me later that it started to hurt at the end. 2 days later she had pain while urinating and got tested for a UTI but it was negative. About a day after the pain while urinating, she began having back pain and now neck pain and a headache. She is a few days past 28, but her cycle is usually 33 or 34 days anyway. What can you tell me about what is going on?