C.G.
Well you can't totally avoid soy, probably. It's in almost everything, even things you wouldn't suspect. If he's eating meat and beans he's getting protein. If he's eating avocado and fish or flax he's getting good fats. Calcium is supplemented in a lot of foods, dry goods, etc, not to mention the fruits and veggies that have calcium in them. If you're really concerned, see your doctor or a nutritionist. I've been told as long as my kids are getting a wide variety of foods and eating lots of fruit and veggies, they won't be deficient. As for calcium, I'm not a big believer that milk is the best way to give calcium anyway ( the vitamins in milk react with each other in a way that actually inhibit absorption) not to mention the fat, cholesterol and sugar levels in milk are astronomical. Even vanilla soy milk has less sugar in it than a regular glass of milk! Do some research, get some good medical advice and go from there my dear.
good luck