You are absolutely right. The latest research is stating that boys and lots of soy is not a good match. Our daughter is very allergic to dairy, for her it's the protein, she gets hives if her skin touches it and vomits if she drinks it.
We give her the Pacific vanilla Almond milk from Trader Joes at $1.69/qt. Almonds are so full of goodness and great fats for the brain, perfect for a growing child. If you're concerned about nut allergies, go for rice milk. Rice milk is cheaper, but doesn't have the good nutrients. Our usual blend is the Silk Soy Plus w/ Omega 3, and Pacific Almond milk 1/2 & 1/2.
Water is truly the best for us to drink. Our latest kick is a recipe for healthy 'koolaid'. Brew hibiscus flowers (very cheap at Food City stores) or another naturally bright red herbal tea like Red Zinger, add a packet of Stevia powder (an herb which is naturally sweet). If it still needs a bit of sweetness, add some Agave Nectar (again from Trader Joes). It's better for the body than honey as the Agave Nectar is lower on the glycemic level than regular sugar or honey.
Best forms of calcium are still the green veg, sesame seeds, etc. Try one of the cookbooks that has you puree veg like spinach and hide it in different foods. Here's the link to her on Oprah showing how she does it.
http://www.oprah.com/slideshow/oprahshow/slideshow1_ss_fo...
Good luck!
L.
~mom to 5yr old ovo-vegetarian who is a 2 yr cancer survivor