In a large skillet over medium heat, cook the pecans until they smell toasted. This should only take a few minutes. Set aside.
Add the butter, white sugar, dark brown sugar, molasses, water and light corn syrup in a large heavy-bottomed saucepan. Over medium heat, constantly stir until the butter melts and turns into one smooth, cohesive mixture.
Clip a candy thermometer to the saucepan. Don't let the bottom of the thermometer touch the saucepan to ensure accuracy. Continue to cook the toffee mixture until it reaches 300 degrees. Stir occasionally. As it cooks, the mixture will turn to a roiling boil and eventually reduce in volume.
As the toffee mixture cooks, stir together the cinnamon, ginger and cloves. Set aside. Line a large baking sheet with parchment paper. Also set aside.
Once the toffee mixture reaches 300 degrees, turn off heat. Stir in the spice mixture, vanilla extract and 1 cup pecans. Carefully pour the toffee onto the parchment paper-lined baking sheet. Sprinkle chocolate chips on top. Allow to sit for three to five minutes. Use a spoon to spread and melt the chocolate on top of the toffee. Continue until the chocolate is fully melted and smooth. Sprinkle with remaining pecans.
All the toffee to sit for at least three hours. Once the chocolate is set, break into pieces. Enjoy!