In a saucepan, cover the beans with 2 inches of water and bring to a boil. Simmer over moderately low heat, stirring occasionally, until tender, about 1 1/2 hours; add water as needed to keep the beans covered by 2 inches. Season the beans with salt and let stand for 5 minutes. Drain the beans, reserving 1 1/2 cups of the cooking liquid.

Meanwhile, preheat the oven to 375 degrees. On a rimmed baking sheet, toss the squash with the oil; season with salt and pepper. Bake for 20 minutes, until browned.

Set a colander over a bowl. In a skillet, cook the clams and 2 tablespoons of water over moderately high heat, covered, shaking the skillet a few times, until the clams open, 5 minutes. Transfer the opened clams to the colander; discard any that do not open. Remove the clams from their shells. Strain and reserve 1 cup of the clam broth.

In a saucepan, brown the bacon over moderately low heat, about 4 minutes. Stir in the butter. Add the onion, celery, and crushed red pepper, cover and cook, stirring, until softened, 8 minutes. Add the garlic, cover and cook until fragrant, 4 minutes. Add the wine and boil until reduced by two-thirds, 6 minutes. Pour in the reserved clam broth, the reserved bean cooking liquid and the cream; simmer for 10 minutes. Stir in the beans, squash, and clams; simmer just until heated through. Serve the chowder in bowls.