Thoroughly pat the squid dry with paper towels. Slice the bodies into 1/2-inch-thick rings and lay on a paper towel–lined baking sheet along with the tentacles; pat completely dry.
Fill a large saucepan halfway with vegetable oil and heat over medium-high heat until a deep-fry thermometer registers 350˚F. Whisk the flour, salt and pepper in a large bowl. Toss the squid in the flour to coat. Transfer the squid to a plate, shaking off any excess flour.
Working in batches, fry the squid in the hot oil until golden, about 2 minutes. Drain on clean paper towels.
Serve the squid with warm marinara sauce and lemon wedges.