In a large zip-top plastic bag, combine 2 tablespoons oil, soy sauce and lemon juice. Add pork and coat evenly. Marinate at room temperature 30 minutes.
Preheat oven to 450F.
In a roasting pan, toss shallots and pears with 1 tablespoon olive oil and 1/2 teaspoon salt. Remove meat from marinade and drain, reserving marinade. Make slits in top of pork; insert sliced garlic and thyme sprigs. Place pork in roasting pan in center of pear mixture. Roast 15 minutes. Reduce oven temperature to 325F and cook until meat reaches 145 to 150F, about 40 minutes.
While meat roasts, melt butter and whisk in flour. Cook over medium heat until golden brown. Pour in broth and reserved marinade; whisk to break up lumps. Cook until thick, 10 to 15 minutes. Stir in thyme. Remove from heat.
Remove pork from oven. Let meat stand 5 minutes before slicing. (If shallots are not well caramelized, remove pork and set in warm place, covered with foil. Increase oven temperature to 400F, place shallots and pears back in oven, and cook until caramelized, 10 to 15 minutes more.)
Reheat gravy over low heat. Add remaining 1/4 teaspoon salt and pepper. Slice pork and serve with gravy.