Broil red pepper on a broiler pan about 5 inches from heat, turning occasionally, about 15 minutes. Transfer to a paper bag, then close and let pepper steam 10 minutes.
When cool enough to handle, peel pepper and discard seeds, stem, and ribs. Dry pepper on a paper towel and purée in a blender until smooth.
Rinse eggplant and dry on paper towel. Heat vegetable oil in a 4-quart pot over high heat until it registers 375°F on thermometer. Fry eggplant in small portions until just golden, about 5 minutes. Make sure the oil stays hot between batches. Drain on paper towels.
Pulse together olives, basil, mint, parsley, marjoram, and 2 garlic cloves in a food processor.
Mince remaining garlic clove and cook in olive oil along with anchovy in a large pot over moderately low heat, stirring, until anchovy dissolves and garlic is fragrant, about 1 minute. Increase heat to medium and stir in pepper purée, then cook, stirring, 1 minute. Stir in olive mixture, capers, and wine and cook, stirring, until wine is evaporated, about 1 minute. Stir in eggplant (sauce will be very thick) and remove from heat. Keep warm, covered.
Cook pasta in a 6- to 8-quart pot of boiling salted water until al dente, then drain and stir into sauce. Season with salt.