Baby Having Watery, Dark Green, Foul Smelling Stools After Changing Formula To Neocate. Got Rash, Runny Nose, Cough. Diagnosed As Bronchitis. Suggestions?

I have a 3 month old daughter who has been having infrequent, watery, dark green, foul smelling stool . She appears to have a lot of discomfort at times. She was breast fed, switched to nutramigen at 6 weeks old when she had blood in the stool and a possible milk protein allergy was detected. She still had blood and mucousy stool and a lot of discomfort while on nutramigen. At 2.5 months of age the pediatrician switched her formula to neocate . As soon as we started neocate her stool stopped having blood but became very infrequent, watery (almost like someone just airbrushed her diaper green). She has been on neocate for almost 3 weeks and while the blood is gone she still has some discomfort. We saw the GI specialist yesterday and they are testing for possible infection and just said its a soy and milk protein allergy but I am wondering if it could be more and would like some thoughts. The doctor didn t order any additional tests. My daughter also recently started getting a rash on her face again and has had a runny nose/ cough the last 2 days. The pediatrician beloved the cough is bronchitis . I have two older children who have been sick with upper respiratory infections. She has not had a fever.