Not sure if I can be of some help, but I will try. My son was very gassy on regular formula, then we switched to another kind he would be great for a week or two and then get really bad again. We were switching formulas like mad. But each time we did, he always got better for a week or two (There must be a reason for that). So when he turned 1 we switched to soy. He still had gas and was constipated. For the constipation we were told to give him a teaspoon or two of Karo syrup in about 4 ounces of water. That worked like a charm! Took away a lot of his stomach issues. But use it only as needed. Then we were told to switch to rice if the soy didn't work. Eventually the soy seamed to be fine. (I didn't realize it was the tiny bit of cheese, yogurt, and occasional scoop of ice cream i gave him was giving him most the trouble) Just make sure he is getting enough fat. Young kids need the fat for brain development. Whole milk has plenty of fat but soy and rice do not. My doctor told me that i should give him buttered crackers, or anything I could find that had lots of fat. Also may or may not work: With both my kids I couldn't have any milk in my diet while I breast-fed. They also could not drink regular formula. But for some reason around 1 to 2 years old, Cow's Milk was fine for them. I don't know why, maybe there little tummies just hadn't developed yet. My son can now have all milk products. I was lactose intolerant till I was 6 years old and then was fine. It doesn't make since, I know. Just keep experimenting.
One more thing: Are you giving him very vanilla, or very very vanilla soy? My son loved the flavored soy milk, not the normal kind. And I'm pretty sure SILK has a vanilla soy that is for kids, with extra calcium. That was the one I used to buy.