In a medium bowl, whisk together flour, baking soda and salt and set aside.
In a large bowl, cream butter with both sugars and vanilla extract by hand using a wide rubber spatula until smooth and slightly fluffed. You can also use a stand mixer with the paddle attachment and beat on medium-low speed for 1-2 minutes. It should look more like a paste or damp sand rather than an aerated mixture. This should only take a minute. Stir in honey. Add the egg and coffee grounds and mix until well incorporated.
Add flour mixture to the butter mixture all at once and stir until most of the flour is absorbed. Before all of the flour is combined, add chocolate chunks and pecans and continue folding them in so they are evenly distributed. You should end up with a soft, moderately moist dough. Place a piece of plastic wrap directly over the surface of the dough in the bowl and refrigerate for at least 2 hours.
When ready to bake, preheat your oven to 350°F and line two baking trays with parchment paper.
Roll approximately 2 tablespoons of dough into smooth balls and place them onto your prepared baking sheets spacing them 2 inches apart. You can also use a 1½-oz trigger or quick-release ice cream scoop to portion mounds of dough. Flatten dough portions slightly with the palm of your hand and bake for 9-11 minutes, until golden around the edges.
Transfer baking sheets to a wire rack and let cookies cool on the trays for 2 minutes before carefully transferring individually to a wire rack to finish cooling.