Heat a large heavy skillet over medium heat. Add guajillo and ancho chiles to the skillet; cook, stirring continuously, 2 to 3 minutes or until fragrant. Set aside.
In a large saucepan over high heat, add 6 cups water and bring to a boil. Transfer the chilies to the water and remove from the heat. Let stand 7 minutes or until the chiles are softened.
Drain chiles and discard water. Hold the tip of the chiles and snip off the stem. Scrap out the seeds. Discard seeds and stem. Add chiles to a blender. Set aside.
Using a paper towel, wipe the large skillet dry. Add 1 tablespoon oil to the skillet and heat until shimmering. Add the tomatoes, onions and garlic. Cook, stirring frequently, until onions and garlic are lightly browned. Add peppercorns, oregano and thyme. Cook, stirring frequently, 9 minutes or until the flavors are melded. Let cool slightly.
Transfer mixture to the blender with the chiles. Add the cumin, apple cider vinegar and 2 cups cold water. Blend about 1 minute or until smooth. Strain mixture, reserving the sauce.
Arrange chuck roast and short ribs in a large nonreactive casserole dish. Season all over with the salt. Pour adobo sauce over the meat and turn to coat with the sauce. Cover tightly and refrigerate 4 hours or up to 2 days.