Preheat oven to 350 degrees.
Line cupcake pan with liners for 12 cupcakes. Set aside.
In small bowl, combine the flours, baking powder, baking soda, cinnamon, salt, cloves, ginger, and nutmeg. Set aside.
In another medium bowl, add softened butter, oil, and brown sugar. Mix well. Add in eggs, vanilla, Greek yogurt, and molasses. This time, only mix to combine. You don't want to overmix it. Last step is the dry ingredients. Add these in and mix again to combine. Be careful not to overmix here! A few small lumps is not a big deal.
Scoop batter evenly into your lined cupcakes pan.
Place in oven.
These will take between 12-18 minutes to bake, depending on the actual temp of your oven.
I like to under bake these just a touch. The reason for this is even after your remove the cupcakes from the oven, they will continue to cook. This is called carry-over cooking. It really important when working with whole grains as they absorb more liquid than refined flours. I test the cupcakes for doneness by touch. This is done by gently pressing in the center of the cupcake. If you can feel it slightly underbaked in the very center of the cupcake, like about ½ inch in the very center, it is perfect. Remove from oven, and the carry over cooking will finish off the last little bit.
Remove from oven. Allow to cool aboout5 minutes in the pan, then carefully remove and place on a cooling rack.
Now, they are ready for icing and doesn't your house smell amazing!!