Preheat the oven to 375°F (190°C). Butter a 9x13-inch baking dish.
Place the sweet potato chunks in a large pot and cover with cold salted water. Bring to a boil over high heat, then reduce to a simmer and cook until the potatoes are completely tender and falling apart, 15 to 20 minutes. Drain very well and let sit in the strainer 2 minutes so excess moisture steams off.
Transfer the hot sweet potatoes to a large bowl and mash until smooth (a hand mixer makes this fast and lump-free).
Whisk in the melted butter, 1/2 cup brown sugar, eggs, milk, vanilla, cinnamon, nutmeg, and 3/4 teaspoon salt until completely smooth and creamy. Taste and add a pinch more salt if needed.
Spread the sweet potato mixture evenly into the buttered baking dish and smooth the top.
In a medium bowl, stir together the chopped pecans, flour, 1/2 cup brown sugar, and 1/4 teaspoon salt. Pour in the melted butter and toss until every crumb is coated and the mixture clumps together.
Sprinkle the pecan streusel evenly over the sweet potato filling, covering the surface completely — crumble any large clumps with your fingers so the topping bakes up crisp all over.
Bake for 35 to 40 minutes, until the streusel is deep golden brown and the edges of the casserole are bubbling.
Let rest 10 minutes before serving — the streusel sets and gets even crunchier as it cools.