Preheat oven to 350 degrees F. Line 2 (12-cup) regular muffin pans with 18 paper cupcake liners.
Add cake flour, baking powder, and sea salt to a small mixing bowl. Whisk to combine. Set aside.
Add fresh lemon juice to milk and set aside for several minutes.
Add unsalted butter and granulated sugar to stand mixer. Beat on medium high speed for about 3 minutes.
Add eggs one at a time, beating on low after each addition for about 30 seconds, or until incorporated.
Add vanilla bean paste and fresh lemon zest. Beat on low for about 15 seconds, or until incorporated.
Add half the flour mixture. Beat on low, just until incorporated, about 30 seconds. Add half the milk mixture. Beat on low, just until incorporated, about 30 seconds. Repeat process with remaining flour and milk mixtures. Avoid over mixing.
Add blueberries and cake flour to small bowl. Toss gently to combine. Remove bowl from stand mixer. Fold in blueberries.
Divide cupcake batter between prepared muffin pans. Bake in preheated oven for 22 minutes, or until cupcakes are golden along the edges, firm to the touch, and a toothpick inserted into the center of a cupcake comes out clean.
Remove muffin pans from oven and place on wire racks to cool.
Remove cupcakes from muffin pans. Cool completely before frosting.