Bring a large pot of water to a boil; season generously with salt. Cook pasta until al dente according to package instructions; drain, reserving ½ cup pasta water.
Melt ½ tablespoon butter in a small skillet over medium heat. Add Panko and cook, stirring constantly, until golden brown and toasted, about 2 minutes. Transfer to a medium bowl.
Add bacon to a heavy-bottomed pot or Dutch oven over medium heat. Cook, stirring occasionally, until fat has rendered and bacon is crisp, 5–7 minutes. Using a slotted spoon, transfer bacon to bowl with breadcrumbs. Stir in ½ teaspoon lemon zest and set aside.
Add bell pepper, shallot, garlic, oregano, and red pepper flakes to bacon drippings and cook over medium heat until vegetables begin to soften, about 2 minutes.
Add clams in an even layer, then stir in wine. Bring to a simmer, then reduce heat to medium-low. Cover pot with a tight-fitting lid and simmer until clams have opened, about 15 minutes. Using tongs, transfer cooked clams to a bowl (discard any that did not open).
Bring clam cooking liquid to a boil over medium heat. Stir in remaining 2 tablespoons butter and reserved pasta water. Add cooked pasta and clams and toss thoroughly, yet gently, to combine. Stir in 2 tablespoons lemon juice and parsley; season to taste with salt and red pepper flakes.
Transfer to a serving dish and sprinkle reserved bacon-breadcrumbs generously over the top.