Place the butter, light brown sugar, granulated sugar, vanilla, cinnamon, nutmeg, ginger and cloves in the bowl of an electric stand mixer fitted with the paddle attachment and mix on medium until creamy and lightened in color, about 4-5 minutes. Scrape sides and bottom of the bowl to make sure everything is well blended.
With the mixer on low add the eggs, one at a time, mixing each completely before adding in the next. Add in the pumpkin and mix for 1 minute more. Periodically scrape down the sides and bottom of the bowl to make sure everything is well blended. It might look a little grainy after adding the pumpkin, that's fine (see note in step-by-step photos). Add in the baking powder, baking soda and sea salt and mix for 10 seconds more.
Add the flour in two batches, alternating with the water, mixing on low and stopping when just combined. Fold in the 1 cup (170 g) chocolate chips. Let the muffin batter sit while the oven pre-heats and you prepare the muffin tin.
Preheat the oven to 425℉ (220℃) and line every other muffin well with a paper liners. Fill each muffin liner almost to the top with muffin batter (about 3/4s full) and sprinkle the top of the muffins with 1 tbsp (11 g) chocolate chips.
Bake for 5 minutes in the center of the oven and then reduce the temperature to 350℉ (177℃) and continue baking for 15-16 more minutes and the tops are puffed up; some might have cracks (that's perfect, I love that!). For best results, bake one muffin pan at a time. Let cool in the muffin tin for about 10ish minutes, then use a butter knife to help get them out to finish cooling on a wire rack.