Make syrup: In a medium saucepan over medium heat, bring granulated sugar and 1 cup water to a boil, stirring occasionally. Add lemon juice. Reduce heat to an active simmer and cook, stirring occasionally, until slightly thickened and reduced to a scant 1 3/4 cups, 10 to 12 minutes. Remove from heat, stir in 1 tsp. orange blossom water, and let syrup cool.
Preheat oven to 350°. Make filling: In a large bowl, combine 1/4 cup of the syrup with remaining 1/2 tsp. orange blossom water, 2 tbsp. clarified butter, and the superfine sugar. Toss with pistachios.
On a work surface, stack the (unbuttered) filo sheets and cut into 3-in. squares, discarding scraps. Fold each stack over on itself to form a triangle and set triangles slightly apart on a buttered rimmed baking sheet. Using a pastry brush, very generously dab tops and edges of triangles with the remaining 1/4 cup clarified butter, letting some flow onto pan.
Bake, rotating halfway through, until medium golden, 15 to 18 minutes. Let stand just until cool enough to handle, about 5 minutes. Gently open a pocket in center of each triangle and fill with a rounded tbsp. of nut mixture. Set each filled pastry back in pan so that it touches the others. Using a soup spoon, evenly coat warm baklava with 1/2 cup syrup. (Save remaining syrup for other uses.) Let stand at least 2 hours for filling to firm up.
*Find orange blossom water at grocery stores with baking and cocktail supplies, and at international markets.
Find ghee at supermarkets and Indian grocery stores, and samneh at Arabic markets; a blend of butter and oil is the most economical, but all-butter tastes the best.
At supermarkets, check packages of frozen, paper-thin filo dough carefully for size (you want sheets about 12 by 17 in.), and buy more than 1 box, as the quantity of sheets per pound varies by brand. To help prevent cracking, thaw in the refrigerator overnight, not on the counter.