Roast jalapenos directly over stovetop gas burner or under preheated broiler, turning with tongs, until skins are blistered all over.
Transfer peppers to small plastic bag and let stand. When cool enough to handle, remove and discard stems, skin and seeds. Chop flesh into fine dice and set aside.
Cook bacon in skillet until lightly browned; transfer with slotted spoon to small bowl. Add breadcrumbs, along with small amount of bacon fat to moisten, combining well.
In medium saucepan, melt butter over low heat. Add flour and whisk to combine. Let cook, stirring, for 2 minutes.
Gradually whisk in milk. Continue cooking, stirring often, until sauce is simmering and thickened. Let sauce bubble gently until quite thick, about 10 minutes longer, stirring often so it doesn’t scorch on bottom.
Remove from heat and stir in cheddar; when cheese is melted, season sauce with salt as needed.
Preheat oven to 350°F. Cook pasta in large pot of boiling salted water until al dente; drain and return to pot. Add cheese sauce and reserved jalapenos and stir together.
Transfer pasta to 2-quart baking dish or six individual ramekins. Top with breadcrumb mixture. Bake for 25 to 30 minutes or until browned on top and bubbling throughout.