Preheat the oven to 350 F/180 C. Line two large baking sheets with parchment paper and set them aside.
Toss the pecans, butter, sugar, cinnamon, and salt together. Bake the pecans on a lined baking sheet for 12-15 minutes. Set aside to cool, then chop the pecans for the cookie dough (reserve some whole pieces for the tops of the cookies).
Melt the butter in a glass microwave-safe dish until just melted (it should be melted but not hot, if it feels warm let it cool briefly). Then whisk in the brown sugar and granulated sugar.
Whisk in the egg, egg yolk, vanilla, and molasses until combined. The mixture should feel and look thicker when it is thoroughly combined.
Fold in the dry ingredients until almost combined. Then fold in the chocolate chips and chopped pecans. Cover the bowl with plastic wrap and chill in the fridge for 30 minutes.
Use a large 3-tablepoon cookie scoop to scoop the dough onto the second prepared baking sheet. Freeze the cookie dough balls for at least 3-4 hours, overnight will give the best flavor.
Preheat the oven to 350 F/180 C. Bake 6-8 frozen cookies spaced at least 2 inches apart. Bake for 12-14 minutes, or until the edges are golden brown but the middle is still pale and underbaked (but not wet).
Pull the tray out of the oven and press more chocolate chips, whole pecans, and a sprinkle of flaky sea salt on top. Let the tray cool on a wire cooling rack for at least 10 minutes, then transfer them to the wire rack to cool completely.
Store leftover chocolate chip pecan cookies in an airtight container at room temperature for 2-3 days. You can store the frozen cookie dough balls in the freezer in an airtight container or freezer bag for up to 3 months!