Preheat oven to 325°F. Drain oil from 1 (8-ounce) jar sun-dried tomatoes to equal ¼ cup; reserve the remaining oil for another use. Chop the drained tomatoes to equal ¾ cup. Add the tomatoes and the ¼ cup oil to a 2-quart baking dish. Stir in onions, garlic, 2 tablespoons each vinegar and water, ¾ teaspoon salt and ¼ teaspoon crushed red pepper; toss to combine. Cover with foil.
Bake, stirring every 20 minutes and covering again with foil after each stirring, until the onions are caramelized, about 1 hour 30 minutes.
When the onions are almost done, bring a large pot of water to a boil over high heat. Add 12 ounces pasta; cook, undisturbed, until al dente, about 9 minutes. Reserve 1 cup cooking water. Drain the pasta and place in a large bowl.
Add the caramelized onion mixture and ½ cup half-and-half to the pasta; stir until combined. Stir in the reserved cooking water, ¼ cup at a time, until the desired creamy consistency is reached. Divide among 6 bowls; sprinkle with ⅓ cup Parmesan, ¼ cup basil and ¼ cup pine nuts.
