Place an oven rack in the center position and preheat oven to 325°F (165°C). Line a 12-cup muffin tin with paper liners and bring cream cheese, sour cream, and eggs to room temperature.
In a medium bowl, combine graham cracker crumbs, 2 tablespoons sugar, and a pinch of salt. Pour in melted butter and stir with a fork until every crumb looks damp and holds together like wet sand.
Spoon about 1 1/2 tablespoons of crumb mixture into each lined cup and press down firmly with the back of a tablespoon or small glass. Bake crusts for 6 minutes, then remove tin and set on a wire rack. Leave oven on at 325°F.
Wash and dry lemons, then zest with a microplane until you have 2 tablespoons of loosely packed zest, stopping before the white pith. Roll zested lemons on the counter, cut in half, and squeeze 3 tablespoons of juice, removing any seeds.
Add softened cream cheese to a large bowl and beat on medium speed for 1 to 2 minutes until completely smooth. Add 1/2 cup sugar and 1 tablespoon flour, then beat for another 2 minutes, scraping down the bowl.
Turn mixer to low speed and add sour cream, lemon juice, lemon zest, and vanilla extract. Mix for about 30 seconds, just until the batter looks uniform and glossy, then scrape the bowl once more.
Keep mixer on the lowest speed and add eggs one at a time, mixing each for only 10 to 15 seconds, just until it disappears into the batter. Do not overmix to prevent puffing and cracking.
Use a cookie scoop or large spoon to portion about 4 tablespoons of batter on top of each cooled crust, filling each liner about three-quarters full. Tap the muffin tin gently on the counter 3 times to release air bubbles.
Place muffin tin on the center rack and bake for 20 to 22 minutes. Do not open the oven for the first 15 minutes. Cheesecakes are done when edges look set and centers still have a slight jiggle; tops should stay pale with no browning.
Turn off the oven and let cheesecakes cool in the muffin tin on a wire rack for about 30 minutes. Once cool, cover loosely and refrigerate for at least 4 hours, or overnight for the best texture.
Lift chilled cheesecakes out of the tin and peel back paper liners just before serving. Top each with a small swirl of whipped cream, a thin lemon slice, and a pinch of extra lemon zest.