Unfortunately, I don't have much to add about an osteopath as the one I went to was a total dud. I think this is another thing you have to go thru several to find a good one and I just can't afford that no matter how much I want to
I've heard it can do wonders, and I've heard it can do nothing. I assume it just depends on the true root of the problem your son is having.
It sounds to me like you have probably found the problem: MPI or MSPI (I personally doubt the lactose intolerance part, but that's just me). I would look at *every single* ingredient for *every single* medicine or supplement he is taking - including the probiotics - to find out if there is any dairy or soy in them. Look it up online, call the manufacturer, whatever you need to do. And if you don't know if an ingredient contains dairy or soy, look up the ingredients too.
And here's another thing that's just me. I wouldn't give my LOs large amounts of any kind of substitute milk (unless I made it homemade like Rebecca's coconut milk, and even then, I'd limit it to a very small amount). Those are full of chemicals and processing, and he's over a year, so he can get all his nutrition from real, whole foods. He doesn't need "milk" if he's getting those same nutrients from foods. If you don't feel comfortable with that, I'd probably opt for trying a hypoallergenic formula rather than almond, soy, rice or any other kind of substitute milk. That's just my opinion though, and lots of people think differently so you have to decide what's best for you and your son.
I do think that you could look at gaps as an option to heal his gut, but even if you decide not to (it's a very hard diet to do right) I think you will be much better off now that you know to avoid dairy and soy.