In a medium saucepan, melt the butter. Whisk in the flour and cook for a couple of minutes. Slowly whisk in the milk until all is smooth. Add salt and nutmeg. Continue to whisk and cook over medium heat until slightly thickened. Turn off the heat. The sauce will thicken some more upon resting.
PREPARE THE MANICOTTI:
In a large bowl, combine the ham, ricotta, cream cheese, Swiss cheese, ¼ cup parsley and a few grinds of pepper. Set aside.
Fill a large saucepan halfway with water and place it over high heat. Add a pinch of Kosher salt and a good drizzle of olive oil. Bring to a boil, and add the manicotti noodles. Turn the heat down so the noodles are not boiling violently, and continue to lightly boil until the noodles are al dente (about 7 minutes). Stir so they don't stick together. You want them firm enough to hold, but not soft enough where they are going to fall apart. They'll soften a bit more when baking in the sauce. Drain the manicotti and place all of the noodles on a nonstick mat to cool.
Preheat the oven to 350℉. Spray a 9x13-inch pan with nonstick spray.
Pour a little bit of the sauce into the prepared pan (maybe a cup), and use a spoon to spread it to cover the bottom of the pan. Use a cocktail fork or spoon to scoop the stuffing into the manicotti noodles. Fill from both sides to get the filling all the way in there. Place the stuffed noodles into the pan. Continue with the remaining noodles, snuggling them up against the others, until all filling and noodles have been used. Spoon the rest of the sauce over the stuffed manicotti noodles, using it to cover all of the noodles. Sprinkle the remaining parsley on top.
Spray a piece of foil with nonstick spray and cover the pan spray-side-down with the foil. Bake for 50 minutes. Remove the foil, and bake for an additional 10 minutes. Remove from the oven and let cool for about 10 minutes, and then serve immediately.
Notes
Leftovers of this manicotti are fantastic. Just heat them up in the microwave the next day!