Preheat the oven to 375°. Butter two 9-inch, deep-dish glass or ceramic pie plates. Spread the challah on a large baking sheet and toast for about 5 minutes, until lightly golden.
Cut the neck from the butternut squash. Peel it and cut it lengthwise into two 3/4-inch-thick slabs. Very thinly slice the slabs into long, thin strips on a mandoline. Peel, seed and cut all of the remaining squash into 1/2-inch dice.
In a very large nonstick skillet, melt 3 tablespoons of the butter. Add the diced squash and cook over high heat until lightly browned in spots, about 3 minutes. Add 1/4 cup of the sugar and cook, stirring occasionally, until just tender and glossy, about 3 minutes longer. Let cool.
In a large bowl, whisk the remaining 1 cup of sugar with the eggs, milk, pumpkin, cinnamon, nutmeg, cloves and salt. Add the sautéed squash and the challah and gently toss to combine. Spoon the mixture into the buttered pie plates and top each with a loose lattice pattern of the squash strips. Brush the strips with butter and sprinkle with sugar. Cover with parchment and bake for 30 minutes. Uncover and bake for 30 minutes longer, until the tops are golden and the puddings are set. Let the puddings rest for 15 minutes.
In a bowl, whisk the remaining butter with the confectioners' sugar, bourbon and pecans. Serve the pudding with the sauce.