In 9 years we have never found a milk substitute. He drinks water and there is one juice I have found that does not have citric acid in it I make him strawberry shakes (strawberry, water and sugar). "Tea" water and sugar.
My allergist explained to me that milk is for baby cows (not humans) and the calcium is an additive and can be found in other sources. When he was 2 years and 9 months, the nutritional specialist and GI doctor explained that he would be able to get enough calories from bacon, yam and water to sustain himself. It sounds crazy to write this now....but in lieu of a tube feeding with a substance that he would only react to, this was worth a shot. Shortly after age 3 he gained banana. It was / has been a very slow road to progress. Although he is able to do a lot more now, although still restrictive enough we can't risk eating out.
Rice milk would be the closest chance we have but he doesn't tolerate sunflower at this time. Other brands have derivates of corn in them. He's also reactive to coconut and almonds.
As long as you are having progress regarding height / weight and your child is happy - I think you are on the right path I did find a calcium supplement from GNC - Calcium Citrate 1000 mg. He takes a 1/2 tab (500 mg) daily as well as Vit D from NOW, probiotic Floragen4kids, and yummy bears organic complete multivitamin. These products have been tolerated very well by him. I met with a couple of dietician's who reviewed what nutrition he was getting and then helped me know what vitamins / minerals we needed to focus on. One was particularly great with helping me come up with creative ways to cook. For example, once he gained rice and tapioca - I'd buy the tapioca rolls / wraps and fill them with rice and bacon and now whatever else he can tolerate. Advocate for you and your child. Sometimes doctors and etc. may not know your needs and I want to empower you to speak up. Tell them if you feel like you are at a loss with creativity and making food fun. I still have days when I struggle and have a silent pity party. But then, I remember where we came from and I start to feel blessed again. There is no other feeling on earth though when you feel trapped in a situation where only time, having hope / pray for things to get better.