Preheat the waffle iron. In a bowl, whisk together the flours, whole oats, baking powder, and sea salt. In a separate bowl, whisk together the milk, eggs, melted butter, maple syrup, and vanilla extract. Pour the wet ingredients into the dry and stir until combined but with a few lumps, being careful not to over mix. If batter is thick, add up to 1/4 cup of milk, one tablespoon at a time, to thin the batter out (it should be pourable but not thin).
Pour half of the batter into the waffle iron and cook per the waffle iron directions. Keep finished waffles on a baking tray in a 200 ̊F oven until ready to serve.
While waffles are cooking, combined the butter, maple syrup, and cherries in a sauce pan or skillet. Half the vanilla bean and scrape out the seeds into the cherry mixture. Heat over medium-low heat until cherries are tender.
Top waffles with cherry mixture, toasted pecans, and extra maple syrup as needed.