Was there any diarrhoea
when you went to the docter ?If diarrhoea has come after medication then its antibiotic related.If Diarrhoea was the main cause of infection then the legs ,arms hurting could be because of electrolyte imbalance
or infection per se where one has generalised malaise and bodyache.If fever has come down and according to your doc it was ear and throat infection
continue the medication with a probiotic
.Also give her ORS and plenty of liquids.If her symptoms continue get her evaluated again and maybe some investigation too this time.