Preheat the oven to 350°F.
Season the short ribs with salt and pepper. Heat a skillet over high heat and sear the short ribs, turning to brown all sides. Transfer to a plate.
Place the carrots, onions, rosemary, thyme, and bay leaf in a braising dish. Place the seared short ribs on top, and add the tomato paste, water, wine, and bouillon cubes, stirring to dissolve the tomato paste.
Braise for about 90 minutes, until the meat yields no resistance when a skewer is inserted.
In a saucepan over medium heat, combine the bechamel, milk, stock and pepper. Bring to a boil, stirring constantly. Turn off the heat and fold in the cheeses and thyme, stirring until melted and smooth.
Boil a large pot of salted water for the pasta. Add the pasta, stirring to prevent clumps. Cook to al dente, according to package instructions, strain and return to the pot, drizzled with oil to prevent sticking.
In a baking dish, combine the pasta and cheese sauce. Top with breadcrumbs and bake for 10-15 minutes, until golden on top and melty.
Top the mac and cheese with pulled short ribs to serve.