Make the custard: In a 2-quart saucepan, whisk together 1 1/4 cups whole milk, 2 beaten egg yolks, 1/4 cup sugar, and 2 tablespoons cornstarch until smooth with no lumps (about 1 minute). Checkpoint: The mixture should look pale and uniform with no visible cornstarch particles.

Cook the custard: Place the saucepan over medium heat and cook for 8–12 minutes, stirring constantly with a wooden spoon. The mixture will start thin, then gradually thicken as it heats. You'll feel more resistance when stirring as it thickens. Keep stirring to prevent lumps or sticking on the bottom. Checkpoint: The custard should come to a gentle boil and coat the back of a spoon.

Chill the custard: Pour the hot custard into a shallow dish (like a baking dish). Press plastic wrap directly onto the surface to prevent a skin from forming. Refrigerate for 2 hours. Checkpoint: The custard should be cold to the touch and firm enough to spread into the pie shell.

Prepare the berry filling: While the custard chills, measure 1 cup of fresh blueberries (about one-quarter of your total) into a 3-quart saucepan. Add 2/3 cup sugar, 3 tablespoons cornstarch, and 1 cup water. Stir well to combine (about 2 minutes) until the cornstarch has no lumps. Checkpoint: The mixture should look thick and purplish with no visible dry cornstarch.

Cook the berry filling: Place the saucepan over high heat and bring to a rolling boil, stirring frequently (about 5–7 minutes). Once boiling, reduce heat to medium and cook for exactly 2 minutes while stirring constantly. The mixture will thicken noticeably and turn glossy. Checkpoint: The filling should look jam-like and coat the spoon thickly.

Finish the filling: Remove from heat and immediately stir in 1 tablespoon lemon juice and 1 tablespoon butter. Stir until the butter melts completely (about 1 minute). Let the filling cool for 5–10 minutes on the counter, stirring occasionally. Checkpoint: The filling should be warm but not piping hot when you fold in the berries.

Add fresh berries: Gently fold the remaining 3 cups of whole blueberries into the warm filling using a rubber spatula. Use a gentle folding motion to keep the berries intact (about 1 minute). Some berries may break slightly, which is normal. Checkpoint: The filling should look studded with whole berries throughout.

Assemble the pie: Spread the chilled custard evenly into your baked and cooled deep-dish pie shell using an offset spatula or the back of a spoon (about 3 minutes). The custard should reach the edges and cover the entire bottom. Checkpoint: The custard layer should be smooth and completely cover the pie shell bottom.

Top with berry filling: Pour the blueberry mixture over the custard layer and spread gently with a spatula to distribute evenly (about 2 minutes). The berries will settle slightly as you spread. Checkpoint: The berry filling should cover the custard completely and be distributed evenly.

Final chill: Cover the pie loosely with plastic wrap and refrigerate for at least 3 hours or until the filling is completely set and no longer jiggles when you gently shake the plate (3–4 hours total). For best texture, refrigerate overnight if possible. Checkpoint: When you slice, the filling should hold its shape and not run.