What is your diagnosis? Dosage for nat phos 6x for infant reflux

Symptoms 
Everything started a month ago with a fever of 102 at night followed by cold like symptoms runny nose, congestion and cough. He got better in 2 days except the cough got worse so I though maybe he will get the mucus out releasing it onto his BM but he never did. I got worried  when he was crying he vomited a yellow liquid and took him to the doctor the next day and the doc wanted to prescribe him antibiotic for strep throat which I refused do to the lack of proof I decided to wait on the lab test without medications. The strep came back negative even when he had an irritated throat.
So I waited for the cough to go away in its on but that didn't happen either 2 weeks later
I started him back on the fermented cod liver oil which the next day he released some mucus onto his BM. And I have continued the same dose I did see some improvement on the cough but not so much. 
I took him to a new doctor which he diagnosed him with reflux by the symptoms and the doctor prescribed him Ranitidine hc1 15mg oral syrup.
Which of course I didn't give to my son because I tough maybe it's just inflammation of the lungs for coughing so much so I will buy a humidifier to help with that but that same night he had vomited forcefully after nursing to sleep and that's when I started researching and found out about nat phos 6x for reflux but didn't know the right dose and I gave my son 1 tablet without diluting it and it made him supper alert even when minutes before he was ready for a nap and it took him almost 2 hours to fall asleep.
I have given him 1 tablet diluted in 5ml of boiled water after 2 more feedings so far and I noticed he got a very runny nose almost like water coming down.

Should I night wean him to help his reflux?
He does nurse for comfort sometimes.
Please I need help with a good diagnose and the homeopathic cure for his problem.
I do not trust the pediatrics I been to because they all want me to give my son medications without a good diagnosis.

Daytime Symptoms
Congestion behind the nose
Very few wet cough followed by him swallowing his spit up.
White thick mucus in the nose
Fussiness
Gassy
Itchy nose
Sometimes he will have normal BM and one day loose ones.
Skin rash in the Chest and back it gets hard as sand paper

Nighttime symptoms
A lot of wet coughs followed by some choking and swallow of his spit up
Wake up and cry every time he coughs
Itchy nose
Last night he vomit all his breast milk forcefully
A lot of sweating (sometimes the sweat wakes him up)
Gassy
Clear mucus in the nose
White tongue 
Wakes up every 1 hour for the first 4 hours of sleep. He is nursed down to sleep at 7:30pm and needs to be nursed back to sleep when he wakes up. He sleeps 10-12 at nightk
Some snoring and wheezing now and then.
 
My sons profile
He is 11 months old 
Very alert and happy baby
He was hard to burp and pass gasses when he was younger.
He still gassy
He did have Colics when he was younger until recently. ( I wonder if he had silent reflux?)
Stopped vaccination at 4 months old. (after finding out about all the toxins in it) and having a high fever on the last one at 4 mo.
Light sleeper wakes up for any noise.
Had mild eczema since 2 months all over the body reacting to any kind of moisturizer even coconut oil. With the exception to breast milk.
Never taken antibiotics
Only been sick with 2 cold and 1 flu
Takes fermented cod liver oil and infant probiotic as supplements 
Mostly breastfed
Eats some meats fruits and veggies along with grass-fed butter and coconut oil and free range eggs.