Return the meat and bones to the pot and cover with water. Bring to a boil over medium-high heat and skim off any scum that rises to the surface. Once no more scum rises, add the vegetables, bay leaves, and thyme. Add more water if needed to fully cover the vegetables. Bring back to a boil, then reduce the heat to low. Season with salt and pepper and cook for 4 hours. Place an upside-down plate over the contents of the pot to help keep everything fully submerged. Taste and adjust the seasoning occasionally, if needed. By the end of the cooking time, the meat should be fall-apart tender.