Silent reflux in 4 month infant

My little one is having health issues. Hoping to get some advice.
It started when she was about 2.5 months old ( She is almost 4 months now). She suddenly started waking after 45 mins when she took naps. She was always a small feeder. She nurses only one side every time. I think she takes about 2-3 oz every time. So she wants to nurse often. Almost every hour or 1 and half hour. Slowly the problem increased. She would be fussy a lot of the time. The pediatrician thought it could be due to colic or teething or reflux or ear infection. They did find a little ear infection so gave her anti-biotics. Since it had been more than2 weeks since all this started, I thought her body is not able to fight it by itself so I reluctantly gave her the Anti-biotics “Amoxicillin”. The following next week, she got her first shots (vaccinations). After that her situation has worsened. She nurses very little, then she will arch her back and fuss or cry. She burps but is still fussy. So I try to walk which she does not like. I try to rock she does not like. I try to nurse again thinking maybe she is still hungry. But she hates it, she arches her back and now cries. I keep her down. She talks and coos for sometime then starts complaining again. She cannot go for her nap. So I try everything again and eventually after trying for an hour or so she falls asleep for her nap. And she wakes up in 30 to 45 mins!! Since she has not completed her sleep she gets tired in an hour again and we go through the same routine. It is exhausting for both of us. I feel miserable that I am not able to help her and also my older child is getting neglected. Want to mention that as she is nursing or after she nurses for a little while, most of the time, she passes gas or small amount of stool with gas or I hear noises from her tummy or sometime she gets hiccups. And because she has not been nursing well, I started getting milk supply issues. Then I have to do pumping to keep the stimulation so the body will get the message to make more. Else the baby gets very upset since now she is not getting enough and the let down is slow. Everything seems to be a mess. I don’t know how long we will carry on like this.
Her night time feedings are better, but now she does not get deep sleep even in the night. After her first waking, she will keep mving he whole body. He eyes are closed but she moves her head side to side, her arms and her legs. Not sure if she is in discomfort. I have tried burping but she does not have any.
The doctor thinks she might have silent reflux since she does not spit out the milk. She will turn 4 months next week. The doctor has given her over the counter medicine that will coat the stomach lining. I do not want to give her any such medications or any of the other anti-acid prescription medications.
Please advice if there is any alternative way to treat her.

Looking forward to your response.