In a mixing bowl whisk together the raw sugar until combined. Add the butter and switch to a hand mixer to blend together thoroughly and form a paste.
To the mixture add the eggs, vanilla and molasses mixing again until just incorporated, be sure to not overmix.
Pour in the all purpose and wheat flours, baking soda, and salt, again beating on low speed with the hand mixer until combined.
Fold in the chocolate chips and make sure they are evenly placed throughout the batter.
Make about ¼ cup sized cookie dough balls and place at least 2 inches apart on a parchment sheet covered baking sheet.
Place a few chocolate chips on top of each dough ball.
Cover in plastic wrap and refrigerate the dough for 30 minutes.
Preheat the oven to 300 degrees fahrenheit.
Bake for 15-17 minutes until the tops of the cookies have set.
They will be lightly browned, but be sure not to overbake as each oven heats differently.
Let the cookies cool for 15 minutes on the baking sheet or on a rack.