Salt the fish fillets with 1/2 teaspoon of the kosher salt then transfer to the fridge while you prepare the remaining ingredients.
Heat 2 tablespoons of the olive oil in a large braiser or deep skillet over medium heat. Add the onions and season with 1/2 teaspoon salt and the 1/2 teaspoon pepper. Once onions start to soften, add the 3 cloves chopped garlic and cook until they just start to color. Add the 3 pounds chopped tomato, 2 tablespoons capers, 2 bay leaves, and 1 teaspoon chopped thyme.
Once the tomatoes are nice and saucy, add the 1 cup tomato puree, the 3 pickled jalapeños, 3 chiles güeros and the 1/4 cup pickled jalapeno juice. Reduce heat to low and let simmer.
Heat remaining 3 tablespoons oil in a separate frying pan over medium-high heat. Add the baby potatoes and fry until golden brown on all sides. Transfer to the sauce to finish cooking.
Once potatoes are knife tender, slide the fish into the simmering sauce to poach. You may have to do this in batches, depending on how large your pan is. Cook until just cooked through and firm, but not hard. How long this takes will depend on how thick your fish fillets are. Taste and add more salt if needed. Top with the 1 cup green olives and 1/2 cup chopped parsley.
Gently remove the fish from the sauce, be careful not to break it, and place on a platter. Spoon sauce and potatoes over the fish and serve with limes for squeezing.