Divide the pizza dough into 8 even pieces and roll into balls. Cover with a kitchen towel and allow to rise for 20 minutes.
While you wait for the dough to rise, scramble the eggs in a nonstick pan over medium heat, seasoning with salt and pepper, to taste. Set aside and let cool.
Preheat the oven to 425 degrees F. Line a nonstick baking sheet with parchment paper.
Gently flatten the dough balls with your palm, and top with the eggs, diced ham, and shredded cheddar cheese. Pull the sides of the dough up and around the filling, pinching to seal. Pull up the perpendicular sides and pinch. Continue until the filling is completely covered and dough is sealed. Place, seam-side down, on the prepared baking sheet and cover with a kitchen towel. Let sit for 15 minutes.
Fill a large pot with 12 cups of water and bring to a gentle boil. Mix in 1 tablespoon honey. Place half of the bagel bundles into the boiling water for 1 minute, turning once halfway through. Remove from the boiling water with a slotted spoon and transfer to the prepared baking sheet. Repeat with the second half of the bagels.
Sprinkle the bagels with everything bagel seasoning and then bake until golden brown and cooked through, about 25-30 minutes. Serve warm, or let cool to room temperature, wrap individually, and freeze for future use.