Preheat oven to 400 degrees F
Mill the flour.
Add baking soda, baking powder, salt, and pumpkin spice into the flour, stir to combine.
Next, add egg, yogurt, sugar, pumpkin, oil, and vanilla. Stir, but don't overmix.
Allow the batter to sit for 10-15 minutes for the fresh milled flour to start absorbing the liquid, and to allow the bran to start to soften.
I like to use the "rice trick". Put about 1 tsp dry rice in the bottom of each muffin well. Then line each well, and pour in about 1/4 cup of batter in each liner.
Bake muffins for 18- 20 minutes, let them sit in pan for 10 minutes, then remove them to a wire rack to cool
(*Optional) Make the Filling by beating softened butter, and slowly adding powdered sugar.
Add Vanilla, and beat until light and fluffy. Now add the softened cream cheese, and beat until incorporated.
After the muffins are completely cool, you can use the back of a spoon to push into the bottom of the muffin, but not all the way through. Make a little "tunnel" in the muffin, then using a piping bag, or a plastic bag, fill the "tunnel" with the filling.