Preheat oven to 425F.
Working lengthwise, slice off the top quarter of each jalapeno. Using a small spoon, scrape the seeds and ribs out of each jalapeno. Finely chop the tops.
Place a large pot of water over high heat to boil. When the water reaches a bubble, salt it well and drop the pasta. Cook to al dente.
While the pasta is cooking, place a medium pot over medium heat with the butter. Add the chopped pepper tops to the butter and soften, 2-3 minutes. Sprinkle the flour over the peppers and cook 1 minute more. Whisk the chicken stock and milk into the mixture and bring up to a bubble. Stir in the mustard, season the sauce with salt and pepper and simmer until thickened, 2-3 minutes. Remove the pot from the stove and stir in 1 cup of the cheese until melted. Add the pasta to the cheese sauce and stir to combine.
Mound up spoonfuls of the mac n cheese in the peppers. Sprinkle them remaining cheese and breadcrumbs, and bake until the tops are golden brown and peppers are tender, about 15 minutes.