I haven't made waffles but. . .
I mill flour for bread in my Vitamixer. I just made a 5 loaf batch and I let the batter with just the whole wheat, flour, oil, salt, water, potatoes and yeast ferment for about 24 hours. I then made bread, adding white flour till it made a damp lightly sticky dough and boy, is that bread good! I am using some hard white wheat; I don't know the brand, but freshly ground wheat is totally different than the whole wheat flour you get in the stores.
If you make waffles, put the batter on the night before (or at least a couple of hours before cooking) so the whole wheat can absorb moisture more fully. I feel you will get a much nicer product.