I can understand your concern but still First thing I would like to tell you is please do trust your doctor and talk to him about all your concern. This platform will not give satisfying answers to your queries as it can not be just one line answer. Breathing problem in new borns can because of so many problems... starting from delayed clearing of fluid from lungs, to infections, to improper development of lung , to heart disease and so on. All these diseases will have different recovery period. So no one will be able to tell you exact days. If you tell the cause one might guess the recovery period but in that case also it depends on so many other factors like his blood pressure , sugar control and feed tolerance. About antibiotics... they are safe and most hospitals use similar drugs as starting antibiotics in newborns. Thirdly... nearly all new born babies do get jaundice which goes maximum at 5-7 days of life. Only your doctor will be able to tell you wether this jaundice is normal jaundice or because of some other illness. There is certain level beyond which normal jaundice requires phototherapy( light therapy) and night requires some other treatment.

Jaundice is quite common in newborn babies (even the ones not on medication) and can be easily treated with phototherapy. The antibiotics you have mentioned are commonly used and have a great safety profile