Preheat the oven to 350°F and line a baking sheet with parchment paper.
In a medium mixing bowl, whisk together the almond flour, coconut sugar, ground flaxseed, and salt until well combined.
Add the 3 tablespoons melted coconut oil, water, and vanilla bean paste to the dry ingredients. Stir with a spatula until a dough forms, then use your hands to gently knead it into a smooth, cohesive dough.
Place the dough between two sheets of parchment paper and roll it out to about 1/8 inch thickness.
Using a sharp knife or pizza cutter, cut the dough into rectangles about 3 1/2 inches long and 3/4 inch wide. Peel away and reserve the scrap dough to reroll for more rectangles.
Slide the parchment with the cut rectangles onto the prepared baking sheet, keeping the rectangles close together, and bake at 350°F for 8 minutes, or until the edges are just lightly golden.
Remove the baking sheet from the oven. While the cookies are still soft, use the knife or pizza cutter to separate them slightly, then let them cool on the baking sheet for 5 to 10 minutes. Transfer the cookies to a wire rack to cool completely and crisp.
Place 2 tablespoons dark chocolate and the 3 tablespoons peanut butter in a small heat safe bowl. Melt gently in the microwave in short bursts, stirring between each, until smooth, or melt over a small saucepan of simmering water.
Stir the chocolate peanut butter mixture until glossy, then let it cool for about 10 minutes until thickened to a frosting like consistency.
To assemble each bar, spread a thin layer of the chocolate peanut butter mixture on top of one cookie wafer. Top with a second cookie, spread another thin layer of the mixture, then place a third cookie on top to create a three layer stack with two fudge layers.
Place each assembled stack on a parchment lined baking sheet and freeze for 20 to 30 minutes, or until very firm.
When the stacks are almost firm, place the remaining 1 cup dark chocolate and 1/2 tablespoon coconut oil in a small saucepan. Melt over low heat, stirring constantly, until smooth, then remove from the heat.
Working one stack at a time, remove the cookie stacks from the freezer and dip each into the melted chocolate, turning to coat all sides, or spoon chocolate over them while holding them on a fork and let excess drip back into the pan.
Set the coated bars back onto the parchment lined baking sheet and refrigerate or freeze until the chocolate shell is fully set and firm.
Drizzle any remaining melted chocolate over the tops of the bars, then chill briefly again before serving.