In a large pot, cook the bacon over medium-high until crispy, about 3 minutes. Add the onion, celery and 1 tbsp. thyme and cook, stirring frequently, until the vegetables are tender, 8 to 10 minutes. Stir in the squash and flour and cook, stirring, until the flour begins to brown, about 2 minutes. Stir in the stock and clam juice and bring to a boil. Reduce the heat to medium-low and simmer the chowder until the squash is tender, 10 to 12 minutes. Season with salt and pepper.
Add the cod, cover and simmer until the fish flakes apart easily with a fork, 4 to 5 minutes. Stir in the cream and cayenne. Divide among bowls and sprinkle with the remaining 1 tbsp. thyme.