To make the miso walnuts, in a medium saucepan or skillet over moderate heat, warm the mirin, the granulated sugar, and the miso, stirring to incorporate and smooth out the ingredients. When the mixture starts to boil, add the walnuts and cook, stirring frequently, until the walnuts are completely coated and the miso mixture has almost all been absorbed by the walnuts, which will take a couple of minutes. They're done when there's only about a tablespoon of the miso syrup in the pan. Remove from heat and let cool, giving them a stir a few times as they cool.
To make the cookies, preheat the oven to 375ºF (190ºC). Line a baking sheet with parchment paper.
In the bowl of a stand mixer fitted with the paddle attachment on low speed, or by hand, cream the butter and sugars until well-incorporated for about 1 minute. Do not beat the mixture until it's too light or overly fluffy, which can cause the cookies to spread too much during baking.
Mix in the egg. Sift the flour and baking soda together in a small bowl then mix that into the dough along with the salt.
Break or cut the walnuts up a little, but not too much, and stir them into the dough, then stir in the chunks of chocolate. You may need to get your hands in there to get everything thoroughly combined, but don't overmix. The dough can be somewhat irregular.
Shape the dough into 5 equal mounds on the baking sheet, each about 6 ounces (180g), placing them evenly spaced apart. Bake the cookies for 15-18 minutes, sprinkling them with additional flaky sea salt after they come out of the oven, if you wish. The cookies are done when they are light golden brown across the tip. Err on the side of underbaking rather than overbaking.