Adjust oven rack to upper-middle position and heat oven to 375 degrees.
MEAT Pulse the pepperoni in a food processor until ground. Add (the already ground) beef and pulse until thoroughly combined. (This will blend the flavors better and also prep the beef so it's more tender rather than 'stringy out of the package when cooked).
Transfer beef mixture to large saucepan. Add the onion, garlic, and spices and cook over medium heat, breaking up mixture with wooden spoon, until beef is no longer pink, about 5 minutes.
Using slotted spoon, transfer 1 cup beef mixture to paper towel-lined plate and reserve.
SAUCE: Add spaghetti sauce to the meat in the saucepan and simmer until heated through (about 10 minutes). Season with salt and pepper to taste. Begin making noodles and filling while sauce is simmering.
NOODLES Pour 2 quarts very hot tap water into 13x9 inch baking dish. Place noodles into the water ONE AT A TIME (so as not to stick to each other). Soak noodles until pliable, about 8-10 minutes.
FILLING In a large bowl, combine all filling ingredients and the reserved meat. Mix well.
ASSEMBLY Drain noodles on place them in a single layer onto kitchen or paper towels. Pour off water and dry baking dish. Spread half of meat sauce over bottom of baking dish.
With the short side of the noodles facing you, spread 1/4 cup of the filling filling across the bottom of each and roll into a tube. Arrange the rolled manicotti, seam-side down, over the sauce in the baking dish. Spread remaining sauce over top. Cover with foil and bake until bubbling around edges, about 40 minutes.
Remove foil and sprinkle with the grated parmesan cheese. Bake uncovered 5 more minutes. ***IMPORTANT*** Let cool 15 minutes.before serving so the cheese 'sets' and is not gooey.