Cook the linguine according to the package directions, reserving 1 1/2 cups of the cooking water.
Meanwhile, in a large skillet, over medium-high heat, fry the bacon until crisp. Transfer to a paper towel-lined plate. Spoon off and discard all but 2 tablespoons of the bacon drippings.
Return skillet to medium heat, add the onion, and cook until tender, 3 to 4 minutes.
Working quickly, return the drained pasta to the pot along with the pasta water, bacon, and onion. Place the pot over low heat and cook, tossing frequently, until heated through. Remove from heat and quickly add the yolks, one at a time, stirring after each addition. Add the Parmesan and 1/2 teaspoon of the pepper and stir until the sauce thickens slightly.
Divide among bowls. Top with additional Parmesan and the remaining pepper.