Line two baking sheets with parchment paper and set aside.
Measure the butter: set aside 1/2 cup (1 stick) butter to remain at room temperature (softened) and use the other 1/2 cup (1 stick) to brown.
Brown the 1/2 cup (1 stick) butter: melt it in a small saucepan over medium heat, stirring occasionally. The butter will foam, then begin to sizzle and smell nutty; brown solids will form on the bottom. When those bits are amber brown and the butter is fragrant (about 2–4 minutes after foaming starts), remove the pan from the heat and immediately pour the browned butter into a heatproof bowl to stop cooking. Let the browned butter cool to room temperature, about 15 minutes.
While the browned butter cools, cream the softened 1/2 cup (1 stick) butter with 1 cup packed light brown sugar: beat on medium speed with an electric mixer (or by hand) for about 2 minutes, until smooth and creamy.
Add 1/2 cup granulated sugar, 2 teaspoons vanilla extract, and 1 teaspoon molasses to the creamed butter and sugar. Add the cooled browned butter (make sure it is fully cooled to room temperature). Beat on medium speed for about 1 minute, until the mixture is combined and slightly lightened.
Add 1 large egg and 1 large egg yolk to the mixture. Beat for about 1 minute, until incorporated.
Add 2 cups plus 2 tablespoons all-purpose flour and 1 teaspoon baking soda. Mix on low speed (or fold with a spatula) just until no streaks of flour remain; do not overmix.
Fold in 1 cup bittersweet chocolate chips, 1/2 cup chopped pecans, and 1/2 cup coarsely chopped pecans with a spatula or wooden spoon until evenly distributed.
Portion the dough: scoop into 2-tablespoon-sized balls and place them on a piece of parchment paper, waxed paper, or plastic wrap. Flatten the portioned dough slightly into a thick disk, then cover and refrigerate for at least 30 minutes (or freeze for 10 minutes) to chill.
When you are ready to bake, preheat the oven to 350°F (175°C). Allow the oven to preheat at least 15 minutes.
Place the chilled dough balls on the prepared baking sheets, spacing them about 1.5 inches apart. If you like visible salt on top, sprinkle a small pinch of coarse sea salt on each cookie before baking.
Bake one sheet at a time (or two if your oven bakes evenly) at 350°F for 12 to 14 minutes, until the edges are golden brown and the centers are set but still soft.
Remove the baking sheet from the oven and let the cookies rest on the sheet for at least 5 minutes, then transfer to a cooling rack to finish cooling (or serve warm).
Store cooled cookies in an airtight container at room temperature or in the refrigerator for up to 5 days.