In a small bowl, stir together the Brown Sugar (2 tablespoon) and Milk (1 cup) until dissolved. In a large bowl, combine All-Purpose Flour (2 3/4 cup), the milk mixture and Instant Dry Yeast (1 package).
Stir until a soft dough forms. Add the remaining flour as needed. Turn the dough out onto a lightly floured surface and gently knead a few times, forming a smooth ball.
Brush the inside of a large bowl with olive oil. Move the dough to the bowl and cover tightly with plastic wrap. Allow to rise in a warm, draft-free area for about 2 hours, until dough has doubled in size and bubbles appear on the surface.
Turn out the dough onto a lightly floured surface. Divide into 4 equal pieces. Lightly dust hands and rolling pin with flour. Roll one of the four sections into a 12-by-4-inch rectangle.
With the long side facing you, gently press 1/4 of the Ham (1/2 cup) and Mozzarella Cheese (1/2 cup) into the bottom third of the dough.
Roll as tightly as possible, starting with the end that has the filling.
Cut into twelve 1-inch pieces and transfer to a baking sheet lined with parchment paper. Repeat with remaining 3 portions of dough. Let rest, uncovered, at room temperature for 30 minutes.
When time is almost up, preheat oven to 400 degrees F (200 degrees C).
Melt the Unsalted Butter (1/4 cup). Bring Water (6 cup) a boil. Add the Baking Soda (4 teaspoon) and reduce heat to a gentle simmer.
Boil pretzels in batches, cooking about 20 seconds each, turning once. They should be slightly puffed. Use a slotted spoon to transfer them back to the baking sheets.
Bake until puffed and golden-brown, about 15 minutes. Brush warm pretzel bites with melted butter and sprinkle with Kosher Salt (1 tablespoon).