Weigh your soft white wheat berries, then mill them on the finest setting.
In a small mixing bowl, whisk together the freshly milled flour, pumpkin pie spice, baking soda, baking powder, and salt.
In a large bowl, whisk together the brown sugar, granulated sugar, melted butter or oil, whole milk, eggs, vanilla extract, and pumpkin puree until well combined.
Pour the dry ingredients into the wet ingredients and gently fold together just until you no longer see any dry flour. Be careful not to overmix the batter.
Let the batter rest for at least 20 minutes, or even longer if you have time, to give the freshly milled flour time to absorb the moisture.
While the batter rests, preheat your oven to 425°F. Line your muffin pan with paper liners or lightly grease the muffin cups.
Divide the batter between the prepared muffin cups, filling each one all the way to the top.
Bake at 425°F for 5 minutes. Without opening the oven door, reduce the temperature to 350°F and continue baking for 15 more minutes for regular-sized muffins or 20 minutes for extra-large muffins.
Check for doneness by inserting a toothpick into the center of a muffin. It should come out clean or with a few moist crumbs.
Let the muffins cool in the pan for a few minutes before transferring them to a wire rack.