Most WDW restaurants have Pacific rice milk that they can use as a milk alternative. The gluten free waffle wix is Bob's Red Mill and unfortunately the first ingredient in that is potato starch. Since you don't need gluten free, with advanced notice they can likely make a mix using regular flour and rice milk (assuming Pacific is soy free; I've never checked as thank goodness for the moment we don't have to avoid that). I don't know though if there will be a waffle press that can be used that is dedicated safe to these allergies that can be used with regular flour as the gluten free waffle press is kept dedicated to gluten free foods. That I think will be the greatest difficulty. Make sure to contact Brenda from special diets (check out the stickies on this board for contact info). With this kind of list of allergies, I'd ask her to note that you'd like to talk to a chef so that you can make sure you can prepare your son for just what he will and will not be able to eat.
I'm also allergic to pork and with advanced notice I've been able to get turkey bacon that tastes and has a texture much closer to regular bacon than the typical turkey bacon. I've never tried at CM but if one place at WDW can get it then I would assume they all can.
The soy cheese that the WDW restaurants have is the one by Galaxy Foods. This company also makes a milk and soy free vegan rice cheese. If you speak with the chef, he may be able to order in some of the rice cheese to make your son an omelette (if that's something that would interest him). Don't mention it to your son unless the chef says he actually can get it in as he may not be able to. In my experience, chefs really do try their bests especially when it comes to kids, but there really is only so much they can do. You may get lucky if you speak directly with a chef. There's no harm in trying; the worst they can say is that they can't do it.
It really does stink, but many gluten free products have potatos. Even the Van's waffles (they're available at a select few locations around WDW) have potato starch. It's as prevalent as rice unfortunately.
Personally, I would change the Rainforest reservation to a Disney owned restaurant, but that's just me. One of the main reasons we travel to WDW is for the amazing handling of food allergies, but Rainforest Cafe isn't Disney owned so they don't have all the alternative foods that you can get elsewhere. They'll make sure his food is safe, but he'll be unbelievably limited in what he can order, unlike other places around WDW that are actually owned by Disney.