Heat 2 tbsp oil in a large skillet over med-high heat. Trim excess fat off of roast, then season the roast on all sides with salt and pepper. Sear all sides in the hot skillet (about 2 mins per side). Place seared roast into the crockpot.
In the same skillet, add the diced onions and saute for 3-5 minutes, until slightly tender. Place in the crockpot with the roast.
Finely dice/mince the chipotle chiles. Place in a bowl with 1 tbsp. of the adobo sauce. In that same bowl, add the lime juice, apple cider vinegar, chicken broth, cumin, ground clove, oregano, garlic and salt. Mix until well-combined.
Add the sauce to your crockpot and cook on low for 6-8 hours, or on high for 4-6 hours.
When cooking time is complete, using two forks shred the beef until shredded finely (or to your liking).