Cook the linguine according to the package directions. Drain, reserving 1 ½ cups of the cooking water, and return the pasta to the pot.
Meanwhile, in a 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 drippings.
Return skillet to medium heat, add the onion, and cook until tender, 3 to 4 minutes.
Working quickly, add the onion, bacon, and reserved pasta water to the pasta pot. Place over low heat and cook, tossing frequently, until heated through.
Remove pot from heat and quickly add the yolks one at a time, stirring after each addition. Add the Parmesan and ½ teaspoon pepper and stir until the sauce thickens slightly.
Divide the pasta among bowls. Top with additional Parmesan and the remaining pepper.