Add the chocolate chips and heavy cream to a microwave-safe bowl, then heat in 20-second bursts, stirring in between, until smooth. Stir in half the vanilla extract once it's fully melted. Cover the bowl and refrigerate for about 30 minutes, until it firms up and is no longer runny.
While the ganache chills, generously butter your ramekins, then dust them with a little flour, tapping out any excess. This step is what keeps your cakes from sticking once they're baked. Skipping it is the single biggest reason lava cakes fail to release cleanly.
In a bowl, whisk together the melted butter, brown sugar, powdered sugar, pumpkin puree, egg, egg yolk, remaining vanilla, and dry milk until combined. Add the flour, pumpkin pie spice, and salt, then whisk just until no dry streaks remain. Try not to overmix, since a slightly rustic batter is exactly what you want here.
Divide most of the batter evenly between your prepared ramekins, filling each about two-thirds full. Spoon the chilled ganache into the center of each one, then cover the exposed chocolate with the remaining batter so it's mostly sealed in. Keep each ramekin around three-quarters full so nothing overflows while baking.
Preheat your oven to 400°F and bake the cakes for about 18 minutes, until the edges look set but the centers still jiggle slightly. Let them cool for two to three minutes, then run a butter knife around the edge and flip each one onto a plate to reveal the molten center.