Cook the pasta according to the package directions.
Wipe out the pot and melt the butter over medium heat.
Add the flour and cook, stirring constantly, for 2 minutes. Slowly add the milk while stirring. Cook, stirring occasionally, until the sauce slightly thickens, 6 to 8 minutes. Add the Cheddar-Jack, mustard, and pepper and stir to melt. Stir in the pasta.
Transfer to a 9-by-13-inch (3-quart) baking dish and cover with the Muenster. Cool completely. Cover tightly with plastic wrap and refrigerate until ready to bake, up to 4 days.
To cook: Bring to room temperature. Bake at 400° F until golden and warmed through, 25 to 35 minutes.
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