Sorry to hear that Hannah. I would go ahead and take the antibiotics, you are early in the cycle and they won't prevent ovulation, implantation or bother fetal development early on.
On the spotting, possible cysts, uterine or ovarian (which could also explain high temps and maybe headaches.)or breakthrough bleeding or ovulation related. Also, still possible pregnancy, least possible option. About 1 in 450ish women do not test positive with urine tests.