Squid ink is as much a food coloring as it is a flavoring element. Work with gloves or over parchment paper to help keep its stain in your food and not on your hands and tools.
Combine seafood stock, water, wine, and saffron in a medium saucepan. Bring to a simmer over high; cover and reduce heat to low. Keep over low heat until ready to use.
Pulse onion, bell pepper, tomatoes, and garlic in a food processor until finely chopped, 6 to 8 times.
Heat 1 tablespoon of the olive oil in a 15-inch paella pan over 2 burners on medium-high. Add shrimp to the pan; sprinkle with 1/2 teaspoon of the salt. Cook until the shrimp are golden on both sides, 1 to 1 1/2 minutes per side. Remove from pan, and set aside.
Add the onion mixture, squid, and remaining 1 teaspoon salt to the pan; cook, stirring occasionally, until nearly all the liquid evaporates, 7 to 8 minutes. Stir in paprika, and cook 2 more minutes.
Add rice and remaining 1 tablespoon olive oil. Cook, stirring constantly, until rice is slightly translucent, about 1 minute. Remove 1/2 cup of stock mixture, and reserve for use in Step 6; stir remaining stock mixture into paella.
Add squid ink, and stir just until rice is evenly distributed. (Do not overstir.) Cook over medium-high, 15 minutes, without stirring. Rotate the pan to ensure even heating. If paella begins to look dry in parts, add reserved stock mixture to that area, 1 to 2 tablespoons at a time.
Add clams, hinge side down, equally spaced around the pan. Cover and cook 4 minutes. Add mussels, hinge side down. Cover and cook another 4 minutes. Distribute shrimp evenly in pan, and cook another 4 minutes, uncovered. Increase heat to high, and cook, without stirring, 2 minutes. Remove from heat; cover with aluminum foil, and let rest 10 minutes. Top with parsley. Serve with lemon wedges.