1In a heavy 4-quart saucepan, cook the bacon over medium heat, stirring occasionally, until browned and crisp, about 8 minutes. Transfer the bacon to a paper-toweled-lined plate, leaving the fat in the pan.
2Add the shallots and 1 Tablespon of the jalapeno to the bacon fat and cook over medium heat, stirring occasionally, until the shallots are softened, about 2 minutes.
3Add the flour and cook, stirring for 1 minute. Gradually stir in all the clam juice (from the cans and bottles). Add the cream, potatoes, and thyme; bring to a simmer over medium-high heat, stirring occasionally.
4Reduce the heat to maintain a simmer, tirring occasionally, until the potatoes are tender, about 10 minutes.
5Add the whole fish fillets and cook for 3 minutes. Stir in the clams and continue stirring until the fish has broken into chunks. Cook until the fish is cooked through and the clams are heated, about another 2 minutes.
6Season to taste with salt and pepper. Serve sprinkled with the reserved bacon and the remaining jalapeno.