Place the raisins in a clean jar and pour in the rum. Ensure the raisins are covered by the rum. Cover the jar and let it sit overnight (the longer they soak, the more concentrated the flavor in the raisins will be). If you don’t have a day to soak the raisins, you can also let them soak while you make the dough.
In a medium bowl, whisk together flour, baking soda, cinnamon, nutmeg, cloves, ginger, and salt. Set aside.
In a large bowl, use a hand-held or stand mixer to beat the butter and sugar together on high speed until creamy and combined, at least 2 minutes. Scrape down the sides and bottom of the bowl as needed.
Drizzle in the molasses and beat until combined. Then, add the egg, egg yolk, and vanilla extract, and beat until combined, about 1 minute.
Gradually add in the dry ingredients and beat until the ingredients are just combined.
Cover and refrigerate the dough for 1-2 hours, until it is completely cool.
While the dough is cooling, make your filling. In a small saucepan, melt the butter and honey together. In a separate, small bowl, stir the arrowroot and lemon juice together until the arrowroot is dissolved. Add it to the saucepan and mix for about one minute. Add all of the contents from the rum soaked raisin jar, and continue cooking until the mixture thickens, 5-10 minutes. Remove from heat, it will continue to thicken as it cools. Allow to cool completely before assembling cookies.
Preheat the oven to 350°F. Line two sheet pans with parchment paper and set aside.
Scoop the dough into 2 ½ tablespoon-sized balls (we used a #24 scoop), and place them on two parchment lined baking sheets. Working one sheet at a time (keep the other sheet pan in the fridge to make the dough easier to work with), split each ball into two, and use the back of a teaspoon to make a small dent in half of the balls of dough. Drop one teaspoon of the filling into the dented dough. Cover with the other half of the dough and roll into a ball. Roll each ball into an egg shape for the best texture of cookie. Repeat for each dough ball. Once you have a baking sheet filled with dough balls, place it in the fridge to chill while you continue assembling more cookies on the second baking sheet.
This step is optional, but highly encouraged. Fill a separate small bowl with white sugar, and roll each ball in the sugar until it is lightly coated. Place dough balls on the prepared baking sheet.
Bake for 10-12 minutes or until edges appear set. Allow the cookies to cool slightly on the baking sheet before transferring to a wire rack to cool completely.
Enjoy the cookies immediately or allow them to cool completely and store in a sealed container for up to 4 days or freeze for up to 3 months.