Add flour and 3/4 tsp salt to the bottom of a food processor. Turn on for 30 seconds. Add eggs, egg yolks and 2 tablespoons olive oil to a liquid measuring cup. Whisk to combine. Add 1/3 of the wet ingredient through the feed. Pulse a few times to combine. Add another 1/3 and pulse again to combine. Add one more time and turn the mixer completely on. Process until a ball of dough forms, about 30 seconds. If the dough does not form in to a ball, add 1 tablespoon of water at a time while pulsing until a ball of dough forms. You don't want the dough to be sticky, so be sure to not add too much!
Turn dough out on to a lightly floured surface. Knead for 7 minutes until dough is smooth and elastic and doesn't stick to the surface without flour. Form into a ball and wrap in plastic wrap. Rest for 30 minutes.
While dough rests start to make the sauce. Bring a large pot of water to a rolling boil. Make a shallow X with a sharp knife on the bottom of each tomato. Drop the tomatoes in the boiling water for 1 minute or until you see the skin start to peel off from the flesh. Remove from water and peel skin off. Add tomatoes to a medium bowl. Use hands to completely crush the tomatoes. Set aside.
Add bacon to a large sauté pan. Turn the heat on medium and render all the fat out of the bacon until crisp. Remove bacon with a slotted spoon and transfer to a small plate. Add remaining one tablespoon olive oil to the pan. Keep the heat on medium and add onion, 1/2 teaspoon salt and crushed red pepper to the rendered bacon fat and olive oil. Sauté until onion is slightly softened, about 3-4 minutes. Add garlic and sauté another 2-3 minutes until both the onion and garlic are soft.
Add the tomatoes along with the reserved bacon, any accumulated fat and remaining 1/2 teaspoon salt back to the pan with the onion and garlic. Bring to a boil and reduce to a simmer. Simmer, uncovered until sauce is thickened, about 30-40 minutes. Also, about halfway through cooking, taste the sauce and season to taste with salt. Once the sauce is thickened, again season to taste with salt. Reduce to low when thickened.
While the sauce simmers, make the pasta. Use the instructions on your pasta machine to make the spaghetti. Make sure to keep the spaghetti floured so the strands don't stick together.
Once the pasta is formed and the sauce is completely thickened and ready to go, bring the same pot of water you boiled the tomatoes in to a boil again - if needed, add more water. Season with salt, it should be as salty as sea water. Add pasta to boiling water, and use tongs to make sure the strands of pasta don't stick together. Cook for 2 minutes. (Please see notes if using dried spaghetti)
Use tongs to transfer the spaghetti to the sauce to finish cooking, make sure to reserve all cooking liquid. Turn the heat up to a medium-low and continue to toss the pasta with the sauce. Once the pasta starts to absorb the sauce, add 1/2 cup of pasta water. Continue to toss and cook the pasta. Again season with salt if needed. If needed add another 1/2 cup of pasta water and repeat seasoning check. (I used about 1 cup of pasta water). Repeat process until the pasta and sauce are homogenized.
Remove from heat and toss with 1/2 cup of cheese. Transfer pasta to a serving dish and garnish with pecorino cheese.