Newborn milk protein allergy / GERD

My son is three and a half months and had runny poop since he was born. He was exclusively breastfed and at two months his poops became diarrhea and watery and caused him to become dehydrated and we had to hospitalize him for IV and TPN. First they diagnosed him with viral gastroenteritis but then they said he has milk protein allergy and we stopped breastfeeding and gave him Elecare formula. Now he is gaining weight and recovering but the formula caused him to spit up and I see many time his moth gets full from a reflux and that causes him to become uncomfortable and fussy. Also he pushes hard for poop or releasing gas sometimes and also scratches his face and throws his legs up in the air because of pain.
Please advise as what homeopathic medication and what dosage and how long should I give him.

Thanks a lot in advance