Heat 2 cups fumet, clam juice or water in a small saucepan. Add saffron, simmer about 5 minutes, remove from heat and set aside.
Heat 1/4 cup olive oil oil in an 8-quart pot over medium-high heat. Add garlic, allowing it to brown for about 20 seconds, then add onions, fennel, and a pinch of salt. Cook until vegetables are softened, about 4 minutes. Add fennel seed, bay leaf and oregano. Stir and cook for 30 seconds. Add tomato paste. Cook, stirring, until paste darkens a bit, about 2 to 3 minutes. Add chopped tomatoes (squeeze them slightly through your fingers to soften first), white wine, pernod and the saffron flavored fish fumet, clam juice or water. Add remaining fish fumet, clam juice or water, whole jalapenos and bring to a boil. Season with salt and pepper. Cook until liquid has reduced by half. Cover pan and simmer for 30 minutes.
Skim the fat from the soup, and add parsley, basil and tarragon. Add clams and simmer until clams open, about 3 minutes (discard any unopened clams). Add crab pieces and heat through. With a pair of tongs, remove crab legs to warmed serving bowls. Place a colander with shrimp in it, into the pot without submerging it completely. When shrimp are just cooked and pink and add to serving bowls. Use tongs to fish out the clams, add to serving bowls. Melt the butter in the broth, stirring as it melts.
Meanwhile, season halibut and scallops with salt and pepper. Heat a skillet over medium-high heat, add 2 tablespoons oil. Cook the haibut and scallops, without stirring, until browned, about 2 minutes. Turn and cook another 30 seconds. Fish will be slightly underdone. Cover scallops and sautéed fish with ladles of broth, bring to a simmer, then transfer scallops and fish to the serving bowls.
Remove bay leaf and the jalapeno peppers from pot. Season broth with salt and pepper. Pour broth over fish in bowls.
Mash the softened jalapeno peppers into a paste, and serve as a garnish for guests who like their Cioppino spicy.
Place all ingredients in a large stockpot. Bring to a boil. Lower heat and simmer for 30 minutes. Strain fumet and allow to cool before storing.
*Michael's note: Always rinse any blood off your fish bones in cold water for a clearer stock. Never use salmon bones for stock, the fish is too oily.