Make the pastry: Heat oven to 350ºF.
Using a coffee or spice grinder, grind the cinnamon stick and whole allspice until fine.
Pulse the almonds, walnuts, pistachios, sugar, and freshly ground spices in a food processor until finely chopped, but not pasty or powdery, about 15 quick pulses. Set aside.
Combine the water and rose water in a small spritz bottle and set aside.
Trim the sheets of phyllo to fit the bottom of a 9-by-13-by-2-inch metal pan. Brush the bottom and sides of the pan with the clarified butter; lay down a sheet of phyllo and brush with butter. Repeat this step 9 more times for a total of 10 sheets of phyllo. Top with one-third of the nut mixture and spread thinly. Spritz thoroughly with the rose water. Layer 6 more sheets of phyllo with butter in between each layer, followed by another third of the nuts and spritz with rose water. Repeat with another 6 sheets of phyllo, butter, remaining nuts, and rose water. Top with 8 sheets of phyllo brushing with butter in between each sheet. Brush the top generously with butter.
Place in the oven and bake for 30 minutes. Remove pan from the oven and cut into 28 squares. Return pan to the oven and continue to bake for another 30 minutes. Remove the pan from the oven, place on a cooling rack, and cool for 2 hours before adding the syrup.
Make the syrup: During the last 30 minutes of cooling, combine the honey, water, sugar, cinnamon stick, and orange peel in a 4-quart saucepan over high heat. Stir occasionally until the sugar has dissolved. Once boiling, boil for 10 minutes, stirring occasionally. Remove from the heat and discard the orange peel and cinnamon stick.
After the baklava has cooled for 2 hours, re-cut the entire pan following the same lines as before. Pour the hot syrup evenly over the top of the baklava, allowing it to run into the cuts and around the edges of the pan. Allow the pan to sit, uncovered, until completely cool. Cover and store at room temperature for at least 8 hours and up to overnight before serving. Store, covered, at room temperature for up to 5 days.