In the same pan, heat 2 tablespoons of extra virgin olive oil over medium heat. Add the onions and season with 1 teaspoon of kosher salt, and ½ teaspoon red pepper flakes (adjust to taste). Cook the onions until they are translucent and very aromatic, about 8 to 10 minutes.
Add the garlic and saute for another 2 minutes. Add the tomato paste and cook for 3 more minutes. Then deglaze the pan with the wine, scraping all the fond from the bottom, and cook for 6 to 8 minutes.
Add the tomatoes and 2 cups of water and bring to a simmer, and then add the meat back to the pan. Simmer, occasionally stirring over low heat until the meat is tender, about 1-½ hours.
Uncover, add the mushrooms and stir in the remaining ¼ cup parsley and basil. Reduce the heat to low; continue simmering, uncovered, and occasionally stirring until the beef is tender and the sauce thickens, ½ hour to 1 more hour. Taste and adjust season if needed.
About 20 minutes before serving, bring a large pot of salted water to a boil. Add the pasta and cook as the label directs. (Here's How to Make Buttered Pasta).
Remove the Beef Braciole from the sauce and transfer to a platter; remove the toothpicks or butcher's twine. Spoon on some of the sauce and garnish with chopped parsley. Serve the Beef Braciole with a side of Buttered Pasta; top with grated Parmigiano-Reggiano cheese.