Wash the fillets under cold water and pat very dry.
Cut them into pieces no larger than 3x4 inches.
Add enough oil to cover just the bottom of a large skillet and heat until the oil is very hot and rippling on the surface.
Dredge just enough pieces of fish to fit in the skillet, shaking to remove excess flour.
Cook for 2 to 4 minutes on each side, depending on thickness, until golden brown.
As the fish is cooked, transfer it with a slotted spatula to an earthenware or porcelain dish.
Season with salt and pepper.
Continue dredging, then cooking, the remaining fish, adding more oil as needed.
Add the remaining oil and onion slices to the pan, stirring to separate them.
Turn down the heat to very low and continue cooking, stirring occasionally, until the onions are very soft and tender, about 15 minutes.
Add the vinegar, turn up the heat, and boil until the liquid is almost evaporated, about 5 to 7 minutes.
Stir in the wine, adjust the heat to medium-low, and simmer for 20 minutes.
Add the water and raisins and simmer 5 minutes longer.
Sprinkle the whole bay leaves and pignoli over the cooked fish and pour over the cooking liquid.
Cover with heavy aluminum foil and let the fish marinate in a cool place for 12 to 24 hours.