If the cough gets worse don't be afraid to go to the doctor. My daughter was allergic to Amoxicillan as well so the doctor just prescribes something without penicillin in it. I wouldn't wait if he just had two ear infections especially since you say he has mucus build up again. You can use saline drops they really help to thin out the mucus. Also I used to elevate the crib mattress by putting a foam wedge or blanket under it. It will help him to breathe easier. Good luck I hope he feels better soon.