Preheat oven to 350°F. Arrange bolillo slices in a single layer on a baking sheet and toast for 10 minutes, flipping once, until dry and lightly golden. Skip this step if bread was dried out overnight.
In a medium saucepan over medium heat, combine piloncillo, water, cinnamon sticks, cloves, bay leaves, tomato, and onion. Stir until piloncillo dissolves, about 8 minutes. Simmer an additional 10 minutes. Strain out solids and set syrup aside.
Butter a 9 x 13 baking dish generously on the bottom and sides.
Arrange a single layer of toasted bolillo slices in the buttered dish. Scatter raisins, peanuts, queso fresco, and Monterey Jack evenly over the bread. Repeat layers until all ingredients are used, finishing with cheese on top.
Slowly ladle the warm piloncillo syrup evenly over the assembled layers. Press down gently with a spoon so bread is submerged and fully saturated.
Cover tightly with foil and bake for 30 minutes. Remove foil and bake an additional 15 minutes until the top is lightly caramelized and edges are bubbling.
Remove from oven and rest 10 minutes before serving.
