Sorry, I've been meaning to get your recipes but I've been slammed lately with a sick puppy and house construction. Quickly here are my thoughts on your last post:
1. Whole wheat flour actually has a higher gluten count then regular flour which should make the cookies denser/heavier. However, I was thinking this weekend that what you may want to try is replacing a portion of the normal flour with quinoa flour (can usually be found in whole foods or the natural section of most supermarkets) since it's a "superfood" and considered one of the best sources of complete veggie protein. I would start by maybe using 3/4 normal flour to 1/4 quinoa to see how it works
2. If the baking powder or baking soda is off then you'll definitely change the consistency of the cookie. Assuming you kept those the same, my guess is that the added water may have been too much as water will make baked goods "puff up." If you want to keep the soy powder my suggestion would be to either use a little extra milk as opposed to water, mix the soy powder with the milk and then combine it with the cookie ingredients or add some soy powder to some milk and brush it over the top of the cookie before it goes in to bake (though this will make the tops brown faster so keep an eye on them).
3. Keeping in mind that I don't cook with soy powder in our commercial kitchen, my guess is that there's a chance the soy powder is the cause of the fluffiness. Though the only reason I say that is that I've seen what soy powder does to my smoothies which is why, if you want to keep it in the recipe, I may try adding it to the top of the cookie instead so as not to totally impact the structure of the cookie itself.
Baking really is a science whereas savory cooking is much more of an art. Sadly, we pastry chefs can't just throw things together and hope it'll work out - it's all very careful measuring and A LOT of trial and error. We make up for the artistic portion with the fact that we can use a pastry bag to decorate things like no body's business. ;)