Preheat oven to 350°F (175°C) and place cupcake liners in 4 6-count muffin tins. Roughly chop the prunes and set aside.
In a large mixing bowl, stir together the olive oil, eggs, and sugar. Fold in the chopped prunes, then add in the buttermilk and ¼ cup of the orange juice. Gently stir to combine.
In a separate bowl, sift together the flour, baking soda, salt, cinnamon, cloves, allspice, and nutmeg. Use a spatula to fold the dry ingredients into the buttermilk mixture, just until evenly combined, then stir in vanilla extract.
Divide the batter amongst the prepared cupcake lines, filling each no more than ¾ of the way to the top. Bake 30-35 minutes, until a toothpick pulls clean from the center.
While cupcakes are baking, make the glaze and steeped prune topping.
In a small saucepan, mix the buttermilk, honey, orange zest, orange juice, granulated and powdered sugars, and baking soda. Bring to a gentle simmer, then turn off the heat. Melt in the butter and add vanilla extract, stirring to combine, then keep warm.
In a separate sauce pan, combine the wine, prunes, orange juice, and orange zest. Heat to a simmer and cook 2-3 minutes, until the prunes have softened.
Once the cupcakes have baked, remove tins from the oven and poke each cake several times with a fork. Spoon warm glaze over the cupcakes, allow to cool slightly, then repeat two more times.
Top each cupcake with a wine-steeped prune, and serve warm!