In a blender, combine the garlic with the scallions, thyme, black pepper, chiles, onion, bell pepper, orange and lime juices, coffee beans and 2 teaspoons of salt, and puree.
Transfer to a resealable plastic bag. Add the pork shoulder cubes to the bag and turn to coat. Refrigerate the pork overnight.
Preheat the oven to 325 degrees F. Remove the pork from the marinade and transfer to a Dutch oven or covered casserole dish. Add the water and bring to a boil. Reserve the marinade.
Cover and braise the pork in the oven for 1 hour and 30 minutes, stirring the cubes a few times, until tender; transfer them to a bowl.
Boil the braising liquid until reduced to 1 cup. Strain into a saucepan and boil until reduced to 1/2 cup. Add the marinade and boil for 1 minute.
Lightly season the pork with salt and add the reduced sauce. Stir well. In a nonstick skillet, heat the vegetable oil. Add the pork and cook over medium-high heat until the cubes are browned and glazed, about 2 minutes per side, then serve.