For the ginger syrup:
Bring all the ingredients to a boil in a small saucepan and cook until the sugar has melted and the mixture thickens slightly. Remove from heat and infuse for 30 minutes. Remove ginger just before using.
For the cupcakes:
Preheat oven to 350 degrees F. Line 12-muffin tin cups with paper cupcake liners and spray the inside of each liner and the top of the pan with nonstick cooking spray.
Sift together the flour, baking powder, baking soda, salt, ginger, cinnamon and cloves into a medium bowl.
Whisk together the melted butter, brown sugar, eggs, and molasses in a large bowl until blended. Add some of the water to batter then some of the dry ingredients to the batter. Continue alternating with the water and flour until everything is added and smooth.
Fill each paper liner with 1/3 cup of the batter, about 1/4-inch below the top of the liner.
Place into preheated oven and bake just until the tops feel firm and a toothpick inserted into the center come out clean, about 15 to 18 minutes. Remove from the oven and brush the tops liberally with some of the ginger syrup.
Allow cupcakes to cool prior to frosting."