Bring a large pot of water to a rolling boil. Drain and rinse the grape leaves and submerge them in the water to soften in three batches, for 2 to 3 minutes per batch. Transfer to a colander with a slotted spoon. Rinse several times under cold water and drain.
In a 12-inch heavy skillet with a-lid, heat 1/3 cup of the olive oil over medium heat. Add the onions and scallions. Turn the heat to medium low and cook, stirring occasionally, until the onions are very soft and translucent, about 12 minutes. Add the garlic and stir for 1 minute. Add the rice and cook, stirring constantly, for 3 minutes. Add 1 tsp. salt, a few grinds of pepper, and 1 cup water. Increase the heat to medium, cover, and simmer until the water is absorbed, 5 to 7 minutes. Remove from the heat and let cool. Fold in the herbs, pine nuts, and lemon zest and season with a little more pepper.
Set aside any grape leaves that are too small or too irregular to roll. Arrange the remaining leaves, vein side up, in rows on a large surface. Snip off any stems. Pour 2 Tbs. of olive oil onto the bottom of a large (preferably 3-quart) saucepan. Lay four or five of the most irregular leaves, overlapping, over the oil, covering the bottom of the pot.
Arrange about 1 heaping Tbs. of the rice mixture (less if the leaves are very small) across the bottom center of a leaf. Fold the left and right sides over the filling and roll up, gently but tightly, until you have a small log resembling an egg roll. Set it seam side down in the pot. Repeat with the remaining stuffing and leaves, snuggling the rolls closely together. Start a new layer when the bottom is covered.
Drizzle the remaining 1/3 cup olive oil and the lemon juice over the grape leaves. Sprinkle on a few pinches of salt. Cut a piece of parchment to fit tightly over the surface of the leaves and set it on top. Put a heatproof plate that fits inside the pot on top of the parchment, to weigh down the leaves and keep them from opening while cooking. Slowly pour in enough water to just cover the grape leaves. Bring to a boil, lower to a simmer, and cover the pot. Simmer over low heat until the leaves are tender and the rice is thoroughly cooked, 45 to 60 minutes. (By the time the leaves and rice are cooked, most of the liquid will have been absorbed). Remove the stuffed grape leaves from the pot with a slotted spoon, cover with damp paper towels and plastic wrap, and let them cool to room temperature. Serve with the yogurt on the side.
These can be made up to three daysa ahead and refrigerated. Bring to room temperature before serving.