Prepare the oven and baking sheets. Preheat the oven to 325°F. Line two baking sheets with parchment paper.
Make the dough. In a stand mixer or with a hand mixer, cream the butter and brown sugar until light and fluffy. Slowly mix 2 cups of flour on low speed until crumbly (the dough will appear dry but come together). Then, turn the dough onto a floured surface and knead in the remaining ¼ cup of flour by hand until it forms a cohesive dough.
Shape and chill. Shape the dough into a 2-inch-wide log using your hands. Then, wrap the log in plastic wrap and chill for 10-15 minutes if the dough feels soft, making it easier to slice.
Slice and arrange. Unwrap the dough and cut into ½-inch thick slices. Arrange the slices on the prepared baking sheets, leaving ½ inch of space between them (the cookies will not spread much).
Bake the cookies. Bake in the oven for 17-20 minutes or until the edges and bottoms are golden brown. Allow the cookies to cool completely on a wire rack before proceeding to the next steps.
Prepare the caramel topping. Place the unwrapped caramels and heavy cream in a microwave-safe bowl. Heat on 50% power in 30-second intervals, stirring after each interval, until the mixture is smooth and fully melted. Spoon about 1 teaspoon of caramel onto each cookie and gently press a pecan half into the center of the caramel. Allow the caramel to set.
Prepare the chocolate topping. In another microwave-safe bowl, combine the chocolate chips and shortening. Melt on low power, stirring every 20-30 seconds, until smooth and glossy. Spoon a dollop of melted chocolate onto each cookie. Use the back of a spoon or a small offset spatula to smooth the chocolate evenly.
Set the chocolate. Allow the chocolate to harden completely. If your kitchen is warm, refrigerate the cookies for 15-20 minutes to speed up the setting process.
Serve and store. Once the chocolate is firm, stack the cookies gently in an airtight container. Store at room temperature for up to 5 days or freeze for up to 2 months.