Heat a Dutch oven or wide, low-sided pot over medium heat. Add the bacon and cook, stirring often, until crispy, 5 to 7 minutes. Remove the bacon to a paper towel-lined plate and set aside. Add the onion to the bacon fat and sweat, stirring often, until softened, about 6 minutes.
Add the potatoes, garlic, chile flakes, cumin and half the jalapeno. Stir and season generously with salt and pepper, then cook for 5 more minutes. Add the warm fish stock and bring to a simmer. Cover and cook until the potatoes are tender, about 15 minutes.
Taste the broth and season with salt and pepper. Reduce the heat to low and add scallops, shrimp, clams and mussels and cook, covered, until the scallops and shrimp are cooked through and the mussels and clams have opened, about 5 minutes.
Meanwhile, combine the cilantro, scallions, olive oil, remaining jalapeno and half the lime juice in a blender and puree until smooth.
Taste the stew and season with the remaining lime juice and salt and pepper if needed. Divide the stew among 4 bowls and garnish with the cilantro oil, lime wedges and reserved bacon, cilantro leaves and scallions.