Heat water in microwave 20 seconds on high. Add warm water and yeast to a small bowl. Stir until yeast is dissolved. Let stand 5 minutes.
Add milk, sour cream, oil, and honey. Stir until combined.
Add 2 cups flour. Stir well. Cover and let rise 1 hour. Stir, cover, and refrigerate 24 hours.
After 24 hours, let batter stand at room temperature 20 minutes.
Spray waffle iron with cooking spray. Preheat waffle iron. Stir remaining flour into batter. Add salt and egg. Combine well with a whisk. Fold in cheese, ham, and green peppers.
Cook waffles according to the directions on your waffle maker.