For my ds, he was very very congested until he was taken off of a milk based formula and put on Elecare (amino acid based formula). Poor kid could barely breathe. He also grunted terribly b/c his poor little GI system couldn’t handle the milk proteins he was getting from his formula.
IMO, the best things to do for the congestion are:
1. get the intolerances taken care of. Have her stool tested for microscopic blood (fecal hemoccult test) which is a sign of intolerances. Your pedi should be able to do this for you. Even if the hemoccult comes back negative, try the TED (total elimination diet) if you are breastfeeding and an elemental formula (Neocate or Elecare) for formula feeding.
2. run a humidifier(s) in your home
3. use regular saline and squirt it up her nose and let everything run down the back of her throat. Use a bulb syringe to suction her out minimally (2 or so times per day). Something that is very easy to do is to oversuction which will only make the congestion worse.
Good luck!!