In a food processor, blend the first 10 ingredients (chipotle peppers through sugar) until a thick paste forms. Gently toss the tofu cubes with the chipotle sauce and spread on 1/3 of a parchment paper lined baking sheet.
Arrange the bell pepper slices and onion wedges on the remaining area of the baking sheet. Bake for 30 minutes.
Divide the chipotle tofu and vegetables amongst the tortillas, squeezing a lime wedge atop just before serving.