My DD is on Alfamino. She is now 15 months and we have found, through weaning, that she is not only cmpi, but also has multiple other intolerances, and also a couple of actual allergies.
It has been a nightmare! She tolerates Alfamino, but only with Gaviscon to thicken it ( and then lactulose to deal with the consequent constipation ). We didn't delay weaning, which I am quite glad about, as dealing with her many reactions to foods has been very hard.
It is possible your DS is intolerant of one of the ingredients in Alfamino, eg possibly the rapeseed oil. While it is not at all common to be intolerant to that or the other oils in it, it does happen. My DD is allergic and intolerant to quite a lot of vegetables and fruits, which is quite unusual. The reaction a few hours after the milk makes me suspicious he is intolerant to something in it.
Have you had a referral to an allergy clinic? That is what I would ask for next, in your shoes. They can test for allergies, though not intolerances, which is unfortunately a trial and error thing.
The other thing is possibly to ask to try Omeprazole, if he hasn't ready. It is stronger than Ranitidine and will reduce the acid the stomach produces, rather than neutralise it.
I really hope you get somewhere soon. It is very upsetting to see them suffer like that.