Mix the cocoa with the hot water and add the chipotle peppers, chili powder and cayenne. Let steep for 10 minutes.
In a standing mixing bowl, add the sugar, flour, baking powder, baking soda and salt. Mix on low for 30 seconds. Add the oil to the dry ingredients and mix for 1 minute on low. In a separate bowl, lightly mix the vanilla and eggs. Then add to the mixer and blend until incorporated. Add the cold water and the cocoa mixture to the mixer, a little at a time, until incorporated. Scrape the bowl and mix on low for 1 minute.
Fill cupcake liners two-thirds full and bake until done, about 20 minutes.
To assemble: Cool the cupcakes completely and top with the Lime Buttercream and dip in the cooled Chocolate Ganache.
Mix the butter until it is smooth, scraping the bowl every couple of minutes. Add the sugar, and mix until smooth. Then add the vanilla, lime zest and juice. Beat until smooth and creamy. Yield: 6 cups.
Put the chocolate in a stainless steel or glass bowl. In a saucepan, heat the heavy cream until just before a boil. Remove from the stove. Pour over the chocolate, and mix until all the chocolate is melted. Set aside to cool.