Bring a medium saucepan of salted water to a boil. Add the pasta and cook as the label directs. Drain and set aside.
Meanwhile, fry the ham in a skillet over medium heat, turning, until crisp, 2 to 4 minutes. Drain on paper towels, then crumble.
Combine the pasta, tomatoes, red onion, capers, parsley, garlic, lemon zest, cheese and half of the crumbled ham in a bowl.
Make the vinaigrette: Toast the fennel seeds in a dry skillet over medium heat, about 2 minutes. Transfer to a cutting board and crush with a skillet. Whisk the olive oil, vinegar, lemon juice, rosemary, oregano, crushed fennel, 1/4 teaspoon sea salt and the red pepper flakes in a bowl. Pour over the pasta mixture and mix until combined.
Carefully stuff the pasta salad into the peppers using a small spoon. Top with the remaining crumbled ham.