Bacterial infection or Reflux?

Ok so a month ago when Malik was around 6 weeks a friend with a bad flu came to visit.. So as expected Malik and I caught the cold. Malik didn't get any fever just severe caughing and a runny nose. A week later the caughing got better n is almost gone. But now at 11 weeks he's got severe projectile vomiting after almost every feed. Took him to his regular dr and he thinks it's reflux asked me to give him 1.5 mls of motilium 3 times a day b4 feeding. So I did and the symptoms disappeared so against drs request I intentionally missed a dose to c if it's gotten better but nooo still excessive vomiting. So I decided to take him to another dr to c if it's anything else, "note that this dr didnt notice the granuloma he had in his belly which is y I doubted him n took Malik to another dr" well. After check up she thinks that the runny nose he still has + the caugh he has had and the phlegm that's still in his chests seems to b interconnected also the eye infection he was born with!! and she prescribed anti biotics! So now I'm confused as to go with which dr. Baby didn't get a fever at all throughout the month so how could this b an infection? Reflux; does it cause this much vomiting? Baby's weight has been fine and nappies r fine too. So should I follow? I'm leaning towards giving him motilium rather than giving him antibiotics and that's mainly bcuz he doesn't have a fever. Calling out all my mh friends. All comments r appreciated thanks!