For the crust, by hand or using a food processor combine all the dry ingredients until well blended. Add the vanilla and butter, pulsing to combine. If needed, add 1 Tbsp of the milk at a time with the machine running until dough just begins to clump.
Press dough into a greased/lined 9x9 baking dish and chill for 30 minutes to allow the flours to absorb the moisture (prevents a gritty texture). Bake at 350°F for 25 minutes, or until lightly browned.
For the filling, combine all ingredients and mix until smooth. Pour over crust.
Once the pecans are chopped, place them in a sieve and shake out the fine pieces/dust (discard). Evenly sprinkle the nuts and chocolate chips over the filling and bake for another 20 minutes or until edges are set and middle is just a bit jiggly.
Cool completely before removing from pan and cutting.