can have a waxing and waning course so you need to take your medicines sos whenever the pain increases. Secondly what I feel is that as your urine had some infection then you get it checked again and the culture will show us whatever its growing.
For stool and stomach pains it again looks to me like an infection due to some parasite. It will be better to start tablet ofloxacin
combination for about 5 days and see a physician if not cured