To make the fresh whole wheat flour, place just over 1 1/4 cups of the whole wheat berries into a powerful blender. Blend for at least a minute, or until you have a fine flour. Measure out 1 1/2 cups of the flour and set aside. If you don't quite have 1 1/2 cups of flour yet, blend the remaining wheat berries as needed. (See note.)
Dissolve the yeast in the water in a large non-metal bowl. Use warm water between 105 and 115 degrees F. You can judge this by splashing a bit onto the sensitive skin of your inner wrist—it should feel warmer than lukewarm but not hot or painful. Let stand for 5 minutes.
Stir in the freshly ground whole wheat flour, rice flour, and salt until well blended with the dissolved yeast.
Cover the bowl and place it in a warm location until the flour mixture has almost doubled--at least 1 1/2 hours if using quick rise yeast, or 3 hours if using regular active dry yeast, up to 8 hours. (See notes.)
Then cover the bowl loosely with plastic wrap or a plastic bag, and place in the refrigerator, until roughly 48 hours past the time you initially combined the ingredients.
Take the yeast and flour mixture out of the refrigerator and allow to stand at room temperature for 60 to 90 minutes to warm up slightly.
After the yeast and flour mixture has stood for at least an hour, combine the soymilk, oil, maple syrup, baking powder, and baking soda in a small bowl. Mix thoroughly, breaking up any clumps of baking powder or baking soda. Immediately pour into the raised flour mixture and stir until well blended. Let stand for 15 minutes.
Preheat the waffle iron for 3 to 5 minutes while the batter is standing. Spray both grids of the waffle iron with oil. Pour or ladle the batter into the center of the iron, covering no more than two-thirds of the iron’s surface for the first waffle. Adjust the amount as needed for subsequent waffles. Bake each waffle for 3 to 5 minutes, or until it can be removed easily.