Mix the Dry Ingredients - Whisk flour and baking soda together in a medium bowl, and set aside.
Brown the Butter - Cut the butter into 14 even-sized pieces. In a medium skillet, melt 10 tablespoons of butter over medium heat, about 2 minutes. Continue cooking, swirling pan constantly until golden brown and a nutty aroma forms, 1 to 3 minutes. Remove the skillet from heat. Stir the remaining 4 tablespoons of butter into warm butter until completely melted.
Mix the Butter and Sugars – In a stand mixer fitted with the whisk attachment, add the browned butter to the mixing bowl. Add the granulated sugar, brown sugar, salt, and vanilla. Whisk on medium speed (setting 5) until combined, 30 seconds.
Whisk and Rest – Add the whole egg and yolk to the mixing bowl. Whisk on medium-high speed (setting 8) until smooth with no sugar lumps remaining, about 30 seconds. Let the mixture stand for 3 minutes.Repeat the whisking and resting process 3 more times: 30 seconds mixing at medium-high speed and 3 minutes of rest. After four total times, the mixture should be thick, smooth, and shiny.
Add the Flour, Chocolate, and Nuts - Using a rubber spatula, stir in the flour mixture until just combined. Stir in 1 ¼ cups chocolate chips and pecans, and ensure no flour pockets remain.
Chill the Dough – Transfer the mixing bowl to the refrigerator or freezer. Chill until the dough firms up, around 65 to 70ºF (18 to 21ºC), about 15 to 30 minutes. The dough should not feel overly sticky.
Preheat the Oven - Adjust the oven rack to the middle position and heat to 375°F (191ºC).
Roll Out Dough Balls – Divide the dough into 16 portions, each about 3 tablespoons (about 60 grams, 2 ounces), and roll into a ball. If the dough starts to warm and get sticky, place it on a sheet tray and refrigerate for 15 minutes.For a rustic appearance, tear the dough balls in half, then press the two halves together again with the lumpy torn sides facing upward to expose the chips. Shape the sides of the dough back into a circle. If desired, use the remaining ¼ cup of chocolate chips and press some on top.Arrange dough balls at least 2" apart on lined baking sheets, 8 portions per tray. Smaller baking sheets can be used but will require baking in 3 batches. The dough should be room temperature or just below for even cooking, around 65 to 70ºF (18 to 21ºC).
Bake the Cookies – Bake one tray at a time in the center position. Bake for 5 minutes, then rotate the baking sheet. Continue to bake until the cookie edges are golden brown and the centers look slightly underdone, about 5 to 7 minutes. The color will continue to darken during cooling.
Let Them Cool - Leave the cookies on the baking sheet to cool for 3 to 5 minutes, then transfer them to a wire rack. Make sure the oven returns to 375°F (191ºC) before baking the remaining tray.
Notes
Salt Substitution: Use 3/4 teaspoon table salt for kosher salt.
Make Ahead: Refrigerate dough balls for up to 1 week, or freeze for up to 2 months.
Storing: Store cookies in an airtight container for up to 5 days.
Freezing: Store in a resealable plastic bag or airtight container for up to 1 month.