Thanks for the query
Presence of pus cells in fair no. suggests infection. Trace reducing substance in stool is normal finding, if it is more than or equal to 3+ then further evaluation is needed. pH more than 5.5 on cow's milk and 5 on breast milk is also normal. Trace mucus is important as it is associated with plenty of pus cells, otherwise this is also normal. If feeding is normal and baby is active and there are no other obvious symptoms so one should try to find the source of fever
and by that time managing it with antipyratics only. She has already received a course of antibiotic so I would suggest you to repeat the stool test
and consult a pediatrician
so that he will recommend some useful investigations to rule out infection.
I hope this answers your query well
Wish you and your family good health