For the cupcakes: Preheat oven to 350 degrees. Line muffin pans with paper cups. Over a double boiler, melt the cholaca wafers and keep warm. If you do not have a double boiler, you can use a heat safe mixing bowl placed over a saucepan with water. Be sure the bowl does not touch the water. In a separate bowl, sift the dry ingredients. In a mixing bowl fitted with the paddle attachment, add all of the wet ingredients except the melted chocolate. Mix on low speed to combine. Add dry ingredients, mix on low speed until nearly incorporated. Scrape the bowl and mix on medium speed just until fully combined and the batter is mostly smooth. Add the melted chocolate and mix on low speed until fully incorporated. Scrape the bowl and mix once again to ensure and even mix. Portion into paper cups, filling each cup only 2/3 full. Bake 15-18 minutes, until the cake springs back when pressed or a cake tester inserted comes out clean. Cool completely.
For the filling: Place all of the ingredients in a saucepan over low heat. Stir occasionally to prevent burning. Once a sauce begins to form, turn the heat to medium high and bring to a boil. Return to a simmer, and cook until the cherries have begun to break down and the sauce has thickened. Cool completely. Process in a food processor or with an immersion blender to make smaller chunks. Set aside.
For the Ganache: Place the baking wafers in a mixing bowl large enough to easily accomodate both the cream and chocolate. Heat the cream in a saucepan just until it begins to boil. Immediately pour the cream over the chocolate and wait 10 seconds. Using a rubber spatula, slowly stir in small circles from the center, working your way to the outsides until the chocolate begins to emulsify with the cream. You are looking for a smooth, glossy texture. To help the melting process with the chocolate, you can also warm it up while you heat the cream. Cool completely. Once the ganache has cooled completely and set, bring it to room temperature. Transfer the ganache to a mixer bowl fitted with the paddle attachment. mix on low speed until the ganache becomes smooth. Scrape the bowl and mix on medium speed for approximately 10 minutes. You are looking for the ganache to be the consistency of buttercream. This may take more or less time depending on the temperature in your kitchen. Scrape the bowl periodically to ensure an even, smooth mixture.
To Finish: Place the filling in a piping bag fitted with a round tip, or a tip made specifically for filling cupcakes. Using a twist tie or rubberband on the end will prevent the filling from oozing out while you fill the bag. Make an indent into the center of the cupcake with the tip, and gently pipe the filling into the cake as you bring the bag upward. It is alright if some of the filling overflows on the top of the cake. Fill each cupcake. Place the whipped ganache in a piping bag fitted with a round or star tip, depending on your decorating preference. Pipe onto cake, remember that a little goes a long way! Serve cupcakes immediately to ensure that the ganache does not set.