For cupcakes:

• Preheat oven to 325 degrees F. Line two cupcake pans with 24 liners. Combine butter and brown sugar in the bowl of a stand mixer fitted with paddle attachment and beat for about 3 minutes until light and fluffy. Add eggs one at a time mixing between each addition and scraping down sides of bowl.
  
• In a separate bowl, mix flour, baking powder, baking soda and salt. Add the dry ingredients and the milk alternately to the mixing bowl beginning and ending with the dry ingredients. Mix until just blended. Mix in the vanilla and chocolate chips.
• Divide batter evenly between the liners. Bake 17-20 min or until a toothpick comes out clean. Remove and let cool for 5-10 minutes. Then remove cupcakes from tins and cool completely before filling and frosting.
• ** I like to fill a large ziplock baggie with batter, remove the air and seal it. Then I carefully cut a corner of the baggie and use it as a pastry bag to fill the cupcake liners with the batter. I find it speeds the process up and I don't spill batter all over the tins.

For the cookie dough filling:

• Place flour in a microwave safe bowl and cook on high for a total of 1 minute and 15 seconds. Do this in 15 second increments, stirring the flour between each.
• Cream the butter and sugars until light and fluffy. Add the heat treated flour and salt and mix until incorporated. Mix in the milk and vanilla and chocolate chips. Cover bowl with plastic wrap and set aside until ready to use. Store in fridge if you're making it ahead.
  

For the frosting:

• Place flour in a microwave safe bowl and cook on high for a total of 1 minute and 15 seconds. Do this in 15 second increments, stirring the flour between each.
• Beat the butter and brown sugar in the bowl of a stand mixer fitted with paddle attachment until light and fluffy for about 3-5 minutes. Add the confectioner sugar and beat on low until incorporated. Scrape the sides of bowl and turn on medium high and beat until smooth. Turn back to low speed and add heat treated flour and salt and mix until incorporated. Add the milk and vanilla and turn back to medium high and mix until nice and creamy.
  

To fill and frost cupcakes:

• Using the back side of a pastry tip ,sink into center of the cupcake to make a well for filling. Roll cookie dough filling into 1/2 inch to 3/4 inch balls and place in the well of each cupcake. Fill a pastry bag with desired tip attached with frosting and frost the cupcakes.

Flour that is not going to be cooked should be heat treated to help kill any possible bacteria that it may contain.