Set an oven rack 6 inches from the heat source and preheat the oven to 425 degrees F.
Bring a large pot of salted water to a boil. Add the macaroni and cook until it is al dente, about 6 minutes. Strain, reserving 1 3/4 cups of the pasta water. Set aside.
Melt the unsalted butter in a large saucepan over medium heat; transfer half the melted butter to a medium bowl and reserve. Add the chopped jalapenos to the saucepan, toss to coat and cook until softened, about 5 minutes; transfer to a small bowl and reserve.
Wipe out the saucepan and add the half-and-half. Cook over medium heat until it just comes to a simmer. Continue simmering until the half-and-half is reduced to 1 1/2 cups, about 15 minutes. Add the cream cheese and stir until melted. Whisk in the Cheddar and Gruyere until all the cheese is melted and the sauce is smooth.
Add the macaroni and reserved pasta water and stir to combine. (The mixture will look very loose, but the pasta will suck up a lot of the sauce as it bakes.) Gently fold in the reserved cooked jalapenos, pickled jalapenos and pickled jalapeno juice. Season with salt and cayenne if needed. Pour into a 13-by-9-inch baking dish. Toss the bread crumbs in the bowl with the reserved melted butter and a sprinkle of salt. Sprinkle evenly over the macaroni and cheese. Lay the sliced jalapenos evenly on top of the bread crumbs. Bake until the cheese is bubbly and the bread crumbs are lightly browned and crispy, about 10 minutes.
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