lack of weight gain in 2 month old

My son is currently 11 weeks old. He was 5 Lbs and 9 oz when he was born. At 7 weeks on Jan 4th, he was 9 Lbs 3.5 oz and the pediatrician was happy with his weigh gain even though he had reflux. The pediatrician said it wasn't interfering with his eating. 2 weeks later, on Jan 16th, at his second month checkup, he was only 9 Lbs 11 oz. This concerned the pediatrician and he said maybe the reflux is affecting his appetite. Around this time, my son also started having bowel movement issues where he wasn't pooping for 4-5 days at a time. However, when he did poop, it was a lot and it was the correct consistency of a breastfed baby - the mushy kind not hard. So my prediatrician prescribed Zantac for the reflux and suggested anal stimulation with a thermometer or a glycerin suppository. My husband and I did not give him Zantac. Instead we did some research and gave him Natrum Phos. This helped my son a lot with his reflux. The not pooping was still a problem. We did the anal stimulation with the thermometer. It worked great the first time. The next time, we had to repeat it after 24 hours and he pooped after another 10 or so hours of doing it. After 2.5 days of not pooping, my son seems to get backed up and dramatically decreases his feeding. Last Sunday, he started having congestion and a wet cough and sneezing. Guess he caught my daughter's cold. So we gave him Nux Vomica when we felt he had the phlegm building in his throat. Other times we gave Euphrasia since he had watery eyes as well as mucous discharge from his eyes. Nux Vomica seemed to regulate his bowel movements so he has been going consistently in the last 4 days. Today he is finally free of his cold symptoms so we haven't given him anything. When I took him to the pediatrician on 29th Jan because of his cold, he was only 10 Lbs 4 oz.

So, the original problem of him not eating enough, remains. Also, in the last one month, its become very hard to burp him after his feeds. He doesn't burp easily. I have been nursing him upright to minimize reflux and we have been holding him upright after feedings for 15 minutes or so each time. He nurses for a bare 5 minutes and doesn't latch on the other side. He is exclusively breastfed. I don't have a lack of milk problem since I am having to pump and store the rest of the milk once he is done nursing.

Could you suggest a remedy for increasing appetite and gaining weight ?
Thank you !