Fry bacon to a crisp in a dutch oven and then place the bacon in a large bowl leaving the drippings in the pot.
Slice the roma tomatoes in half and toss with 2 tablespoons olive oil, 1/2 teaspoon freshly cracked pepper, 1 teaspoon salt, and the leaves from 3 thyme stems. Set aside to rest.
Cube 3 pounds of chuck into 2" pieces.
Sprinkle 2 tablespoons of flour, 1 teaspoon salt, and 1 teaspoon fresh ground pepper over the beef pieces.
Cook the meat at a high temperature in the bacon drippings to brown the edges.
Brown the meat in 2 batches depending on the size of your dutch oven.
After the meat is browned, remove to the bowl with the bacon.
Add 2 tablespoons of butter to the dutch oven, keeping a medium high heat.
Add the mushrooms and a dash of salt.
Brown the mushrooms and add to the beef and bacon bowl.
Melt 2 more tablespoons of butter and add the shallots.
Once they are lightly browned, add the garlic and tomato paste.
Stir and cook for 1-2 minutes.
Add red wine, rosemary, thyme, pepper flakes, and bay leaves to the shallot mixture.
Bring to a low simmer, scrapping up all the browned bits from the bottom of the pot.
Reduce the wine by about a quarter.
After the wine has reduced, add the meat, mushrooms, and bacon to the pot along with 2 cups of beef stock.
Bring temperature up to a gentle boil.
Place the tomatoes on a foil lined cookie sheet skin side down.
Place the cookie sheet of tomatoes and the covered dutch oven in a 300 degree oven and cook for 2.5 hours or until the beef is fork tender.
Uncover the dutch oven and place back on the stove top at a high heat.
Bring to a rolling boil to thicken slightly and skim any fat as needed.
Taste sauce to check if additional salt and pepper is needed.
Stir in the Italian parsley and serve over pasta.
Garnish with the tomatoes, freshly grated Parmesan cheese, and a few parsley and/or rosemary leaves.