Preheat the oven to 350° F. Lightly oil muffin tins or line with paper muffin cups.
In a large bowl, mix together flours, baking powder, salt, and spices. Set aside.
On low heat, melt butter in a small saucepan. Add syrup and honey to the warm butter and stir together. Pour mixture into a bowl and add pumpkin, milk, eggs, and vanilla. Whisk together until well blended.
Add wet ingredients to dry mixture and fold gently, using as minimum strokes as possible. Fold pecans and chocolate morsels into the batter.
Fill muffin cups full with batter and place on middle rack in oven. Bake 25 to 30 minutes. If desired, serve warm with butter. Store leftover muffins in the refrigerator. Makes 15 muffins.