Make the stock: In a pot, combine the water, white fish bones and heads, leek, garlic (for stock), bay leaf, whole black peppercorns, dry white wine, and kosher salt (for stock). Bring to a gentle simmer and cook for 25–30 minutes; strain, stir in the saffron threads, and keep the stock hot at a bare simmer.
Heat the extra-virgin olive oil in a 15-inch paella pan over medium heat. Add the yellow onion and cook until translucent and sweet, 5–7 minutes.
Add the garlic (finely chopped) and cook until fragrant, 30–60 seconds, then stir in the red bell pepper and cook 2–3 minutes to soften.
Stir in the grated ripe tomatoes and sweet paprika. Cook, stirring occasionally, until the sofrito is thick and jammy and most moisture has cooked off, 6–8 minutes.
Add the bomba rice and stir to coat and lightly toast, about 2 minutes.
Pour in 6 cups of the hot saffron stock and season with the kosher salt (for rice). Spread the rice evenly with a spatula and bring to a lively simmer; from this point, do not stir.
After 10 minutes of simmering, arrange the squid and monkfish evenly over the surface so they cook with the rice.
Peel and devein the large shrimp, then tuck them into the rice so they are just submerged; cook until the shrimp are pink and opaque, 6–8 minutes.
Nestle the mussels and littleneck clams hinge-side down into the rice, spacing them around the pan. Continue to cook until the shellfish open and the rice is just al dente with most liquid absorbed, 8–10 minutes; discard any that do not open.
Increase the heat to medium-high for 1–2 minutes to develop a socarrat; listen for a faint crackling and stop before it smells burnt.
Remove from the heat, cover the pan with a clean towel, and rest for 5 minutes. Sprinkle with flat-leaf parsley and serve with lemon wedges.