In a large bowl, combine flour, salt, honey, and yeast. Drizzle in water and stir dough with a wooden spoon until a slightly-sticky dough forms. Cover bowl with plastic wrap and let sit at room temperature overnight or 18-24 hours.
The next day, preheat oven to 425F. Lightly grease a 9-in cast iron with 1 tablespoon olive oil. Punch risen dough down and gently knead in cheddar cubes and jalapeno pieces. (reserve a few for garnishing)
Gather dough into a smooth ball and pat into greased pan Cover with plastic wrap and let rise 30 minutes.
Once dough has risen, lightly brush with remaining 1 tablespoon olive oil and use your fingers to make little indentations all over bread. Sprinkle with reserved jalapeno pieces and cheddar cubes.
Bake focaccia at 425F 30-35 minutes until a light golden brown. (if focaccia is browning too quickly, lightly cover in foil) Cool focaccia 10 minutes before slicing into wedges. Enjoy warm!