In a large bowl, mix yeast, 1 teaspoon brown sugar, and warm water. Mix until sugar is dissolved and let sit about 8 to 10 minutes, until foamy.
In another bowl, mix together remaining brown sugar and milk until brown sugar is dissolved.
Add 2 & 1/2 cups flour and milk mixture to yeast and stir with a wooden spoon until soft ball of dough forms.
Turn dough onto lightly floured surface and knead a few times. Place in clean bowl and cover with plastic wrap. Let sit for 2 hours or until doubled in size.
Turn dough out onto floured surface and divide into 4 pieces. I froze 2 and used the other for the a good sized plate full of pretzels.
Roll each piece into a long rope and flatten/spread out. Place ham and cheese on top of dough and roll up. Seal seam with water if needed. Cut into segments of desired size. Let rest for 30 minutes on baking sheet.
Preheat oven to 400 F.
Bring 6 cups of water to a boil. Lower heat and add baking soda. Cook pretzels in batches of 2 or 3 for about 30 seconds and let rest back on baking sheet.
Bake in oven for about 20 minutes, or until pretzels are light and puffy. Brush with melted butter and top with kosher salt.
You can also make a quick honey mustard dipping sauce by mixing the dijon mustard with the honey.