Place the beef pieces in a large bowl. Season with salt and pepper. Add the flour and toss to coat thoroughly.
In a large pot, melt 2 tablespoons of the butter over medium high heat. Working in two batches to keep them from overcrowding, add the coated beef pieces and cook to brown all the sides, about 8 minutes. Remove to a plate and repeat with remaining beef. Remove to the plate and set aside.
Add the chopped bacon and cook, stirring occasionally, until golden and the fat renders, another 8 minutes.
Add the remaining 2 tablespoons butter, then the garlic and onions. Reduce heat to medium low and cook, stirring occasionally, until the onions are a deep golden color and caramelized, about 30 minutes.
Increase heat back to medium high and pour 1 cup of the beer into the pot, scraping the bottom of the pot to release any browned bits, and cook until it reduces slightly. Add the beef, remaining 1 cup beer, beef stock, sugar, vinegar, mustard, thyme, parsley, bay leaf, and additional salt and pepper to taste.
Bring the mixture to a boil, then reduce heat to medium low, cover, and cook until the beef is tender, about 1 1/2 hours. Discard any stems from the herbs and the bay leaf.
Serve hot with the fries or bread.