Season short ribs with salt and pepper. In a large skillet over medium-high heat, sear the short ribs in the olive oil on all sides until brown. Transfer to the slow cooker.
In the same skillet over medium heat, add the bacon, onion, garlic, and shallots. Cook while stirring occasionally until the bacon begins to brown, about 5 minutes. Pour in the red wine and port and cook until reduced by half, about 5 more minutes. Transfer mixture to the slow cooker.
Add the broth, thyme, and bay leaf to the slow cooker and cook on high for 5 - 6 hours or until the meat is falling off the bone.
Discard the bay leaf and strain the cooking liquid for homemade gravy to pour over top before serving. Season with salt and pepper and garnish with fresh thyme, if desired.