Stir together yeast, 1 teaspoon brown sugar, and warm water in a large bowl and let stand until foamy, 5 to 8 minutes. (If mixture doesn`t foam, start over with new yeast.) In a separate bowl, stir remaining 2 tablespoons brown sugar into warm milk until dissolved. Add 2 1/2 cups flour and milk mixture to yeast mixture and stir with a wooden spoon or rubber spatula until a soft dough forms, adding up to 1/2 cup additional flour, a little at a time, if necessary. Turn out dough onto a lightly floured surface and gently knead a few times to form a smooth ball. Transfer to a clean bowl. Cover with plastic wrap and let rise in a draft-free place at warm room temperature until doubled and bubbles appear on surface, about 2 hours. Preheat oven to 400°F with rack in upper and lower thirds. Line two 4-sided sheet pans with parchment paper. Turn out dough onto a lightly floured surface and cut into 4 equal pieces. Lightly dust your hands with flour, then gently roll and stretch 1 piece of dough to form a 12-inch-long rope. Flatten dough and arrange so a long side is nearest you, then roll out to a roughly 12- by 4-inch rectangle with a lightly floured rolling pin. Gently press one fourth of ham and cheese into lower third of rectangle, leaving a 1/2-inch border along bottom edge. Stretch bottom edge of dough up over filling and press tightly to seal, then roll up as tightly as possible to form a rope. Cut rope into 12 pieces and transfer to a sheet pan. Make 3 more ropes with remaining dough, ham, and cheese and cut into pieces, transferring to sheet pans. Let rest at room temperature, uncovered, 30 minutes (dough will rise slightly). Bring water (6 cups) to a boil in a 4-to 5-quart saucepan. Reduce heat and stir in baking soda. Cook pretzel bites in batches in gently simmering water, turning once, until slightly puffed, about 20 seconds. Transfer with a slotted spoon to sheet pans. Bake until puffed and golden-brown, about 15 minutes (cheese may ooze slightly). Meanwhile, stir together mustard, jalapenos, and honey. Brush warm pretzel bites with butter and sprinkle with pretzel salt. Serve warm or at room temperature with jalapeno mustard for dipping.