Bring a large pot with salted water to a rolling boil. Stir in pasta shells and return to boil. Cook uncovered, stirring occasionally, until the pasta has been cooked through, but is still firm to the bite (about 8 minutes). Drain and set aside.
Heat milk in saucepan until hot, but not boiling.
Melt butter in a saucepan. Cook and stir the onion, garlic, and Cholula Chipotle until the unions are translucent (about 5 minutes). Whisk in flour, 1 tablespoon at a time, and let cook for about 3 minutes, whisking constantly to avoid burnin
Whisk in the hot milk, 1/2 a cup at a time, and stir in smoked paprika, salt, and pepper.
Bring the mixture to a simmer (do not boil), whisking constantly until thickened (about 2 minutes).
Whisk in the cheeses, about 1/2 a cup at a time, and stir until the cheeses have melted and the sauce is thick and smooth.
Stir in pasta shells and bacon gently to combine.