I would wonder reflux pain too. Gaviscon is such a mild medication and not very effective in babies with significant GERD. I'd start there. Around 12weeks is peek time for reflux to act up. It could be his reflux is just untreated.
Wyatt has been on Neocate since 4 months - however he had massively bloody stools (hidden blood, so his stool needed to be tested to see it), and tons of mucous, along with vomiting, and intense bouts of hysterical crying from pain. His bowel was so inflamed, he would grunt constantly because it felt like he had to poop. We have a prescription for the Neocate, and it took 5 months of fighting with the insurance company and an appeal to finally get it paid for. From the company that makes it, Necoate is 36 dollars a can, which makes approx 48ounces of formula. We started with Zantac, then PPI, then Gentlease formula, Alimentum/Nurtimigen, another PPI change (to Prevacid solutabs), and he continued to have bloody stool, so we moved to Neocate and the blood stopped after two months. He was on Zantac twice a day, Prevacid twice a day, and thickened Neocate (to help give it weight so it wouldn't come back up so easy). Recently, we have weaned the Zantac, and stopped thickening the Neocate, and plan to start weaning the Prevacid next month, but he will be on Neocate until after his first birthday, when we will slowly trial milk. I'm glad that his reflux appears to be resolving, and I pray he does well when we trial milk.
Lactose intolerance and milk protein intolerance are two different things. Lactose intolerance being the intestines reaction to the sugar in milk (lactose). MPI is an immune reaction (allergic) to milk protein. Reflux and MPI are also two different things. Sometimes reflux is caused by untreated MPI, but not always - most often its because the muscle that closes over the tummy to prevent the tummy contents (food and acid) from coming up into the esophagus, is immature in babies.
If this is truly a milk protein intolerance/allergy, you will probably need to have baby on Neocate for about a month to actually see results as it takes a lot of time to heal the damaged caused by a true intolerance/allergy.
Is there any way you can see a pediatrician? Or, have a DR test his stool for hidden (Occult) blood. I'd say asking to try Zantac, or a PPI is a fair request from the Dr, and a good place to start at this point.
Best of luck, I hope something here is helpful.