In a heavy pan with a tight-fitting lid, dry-toast farro over medium-high heat until it starts to look and smell toasted, about 2 minutes. Turn off heat and carefully pour in boiling water. Add a pinch of salt, return to heat, and bring to a simmer. Cover pan and cook until farro is tender but chewy, about 15 minutes. Drain if necessary.

Meanwhile, in a large deep pan over medium heat, add oil; add shallots and sauté until they begin to soften, about 2 minutes. Add sliced mushrooms; sprinkle with a pinch of salt and sauté over medium-high heat until mushrooms have released their liquid and are well browned, about 15 minutes. Add garlic and sauté 1 minute.

Mix balsamic and stock together and stir into mushroom mixture. Cook until liquid is mostly evaporated, about 2 minutes. Stir in thyme, and then cooked farro and butternut squash. When farro and squash are heated through, season with salt and pepper and pour into a large serving dish. Top with toasted pecans. Serve hot.