In a medium mixing bowl, whisk the flours, tapioca starch, cacao powder and salt together, then sift. For best results, I strongly recommend that you do not skip this step. It's the best way to ensure that all the lumps get broken down (coconut flour is especially lumpy) and any potential larger pieces or unwanted debris get caught.
Add ghee and honey to a separate bowl and beat on high speed with an electric mixer until smooth and creamy. Add egg, coconut milk and vanilla extract, cream some more until light and fluffy.
Add dry ingredients and mix on low speed until barely just combined, no more. Finish mixing the batter by hand with a rubber spatula or wooden spoon. Transfer the cookie batter to the refrigerator, uncovered, and let it cool for at least 2 hours.
Meanwhile, start working on the chewy caramel: in a medium saucepan, mix the coconut sugar and water listed under “Part I” and bring to a boil over medium-high heat. Let the mixture boil for about 3 minutes, until it takes a really dark caramel color and starts getting thicker.
Meanwhile, in a separate saucepan set over medium heat, mix all the ingredients listed under “Part II” and cook, stirring occasionally, until the mixture just barely starts to simmer then kill the heat. It is important that you do not let this come to a full boil.
As soon as Part I is ready, slowly pour in the warm coconut milk mixture while constantly stirring with a wooden spoon.
Once all the milk has been added and completely incorporated, bring the caramel to a boil and continue cooking for 3 full minutes while stirring constantly, then turn off the heat, transfer to a small bowl and set aside to cool.
When the caramel is cool enough and has the consistency of soft toffee, preheat your oven to 350°F and line a baking sheet with parchment paper.
Roll the dough into 1” balls (roughly the size of a ping-pong ball) and place them at least 1” apart on the baking sheet. A spring loaded ice cream scoop works wonders for this!
Sprinkle each cookie with chopped pecans then make an indentation in their center by pressing down gently with your finger.
Bake the cookies for 8 minutes and remove from oven. Immediately press centers again to recreate the indent. Cool for 5 minutes in the baking sheet and then transfer to a wire rack.
With wet hands, grab about a teaspoon of caramel from the bowl and shape it into some kind of a flat circle. Place that flat circles right into the cookies’ indents. Don’t worry about shaping the centers perfectly; the warmth of the cookies will take care of that for you in just a few minutes. If you find that your caramel is too stiff and won’t flatten nicely, place it in the microwave for just a few seconds (really, a FEW, as in 5 to 10) to make it a tad more pliable, or place the cookies in the warm oven for a minute or two after having placed the caramel centers on all of them.
Lightly press half a pecan over each of the caramel centers and then drizzle with the melted dark chocolate.
Place the cookies in the refrigerator to cool completely and then store in a single layer in a cool, dry place for up to a week.
*You will have leftover caramel, but by all means, don't throw it out. This will keep for quite a while in an airtight container kept in a cool dry place. I'm absolutely certain that you'll find some way to use it up!