In a large bowl, combine water, yeast, honey and olive oil. Mix with a spoon, then let sit until foamy, about 10 minutes. Add in 2 1/2 cups flour and salt, stirring with a spoon until the dough comes together but is still sticky. Using your hands, form the dough into a ball and work in the additional 1/2 cup flour, kneading it on a floured surface for a few minutes. Rub the same bowl with olive oil then place the dough inside, turning to coat. Cover with a towel and place in a warm place to rise for about 1-1 1/2 hours.
Place the pizza stone on the rack in the center of the oven. Preheat your oven to 450 degrees F.
After the dough has risen, punch it down and place it back on the floured surface. Using a rolling pin and your hands, form it into a circle.
Dust the pizza peel with flour or cornmeal. Place the circle of dough on the peel. Brush it with olive oil and cover it with the garlic. Cover the dough with the cheeses. Top with the sliced jalapeños and crispy bacon.
Bake the pizza for 15 minutes, or until golden and bubbly. Remove and slice. Serve!