So based on what you are saying it seems you had an urinary tract infection
(UTI) which was treated with antibiotics. When these UTIs are complicated they can infect not only the bladder, but go up to the kidneys and cause what is called "pyelonephritis", which can cause severe back pain
. Also kidney stones can cause back pain which radiates to the groin. If your repeat urine culture was while you were on antibiotics, it could be a falsely negative result. The fact that you were given multiple antibiotics will alter your normal intestinal bacteria, or "intestinal flora", and you can get diarrhea
, cramps, etc. These should go away on its own, although probiotics may help.
Having an infection can also cause headaches
Hope that helps