[*]1 4-pound beef chuck roast, trimmed of fat (although it is not the leanest cut of beef, chuck is still our choice for pot roast because it doesn't dry out during braising. You will find pockets of fat as you carve it, but they are easy to remove)[*]1/2 teaspoon salt, or to taste[*]Freshly ground pepper, to taste[*]4 teaspoons extra-virgin olive oil, divided[*]2 large onions, halved and thinly sliced (4 cups)[*]4 cloves garlic, minced[*]1 teaspoon dried thyme[*]1/2 cup strong brewed coffee[*]2 tablespoons balsamic vinegar[*]2 tablespoons cornstarch mixed with 2 tablespoons water

Season beef with salt and pepper.
If you perfer your beef browned (I usually no not bother),heat 2 teaspoons oil in a Dutch oven or soup pot over medium-high heat. Add beef and cook, turning from time to time, until well browned on all sides, 5 to 7 minutes
Place meat into crockpot
Add the remaining 2 teaspoons oil to the pot. Add onions, reduce heat to medium and cook, stirring often, until softened and golden, 5 to 7 minutes. Add garlic and thyme; cook, stirring, for 1 minute.
Transfer beef to a cutting board, tent with foil and let rest for about 10 minutes.
Meanwhile, skim fat from the braising liquid. Pour the liquid into a pan. Add the cornstarch mixture and cook, whisking, until the gravy thickens slightly, about 1 minute. Season with pepper.
Carve the beef and serve with gravy.

Am I missing something? To what and when do you add the coffee?  I assume it's for the gravy.

The doffee is added to the liquid in the crockpot for cooking. It darkens and flavors.