I got this out of a taste of home cookbook and it really is delicious. You can make it as spicy as you'd like and it won't effect the recipe. I didn't have any chipotle peppers so I used jalapenos and they worked just as well.
Place the chili sauce, lime juice and chipotle peppers in a food processor; cover and process until blend. Transfer 1/2 cup to a large resealable plastic bag; add chicken. Seal bag and turn to coat; refrigerate for 1-4 hours.
Pour remaining marinade into a small bowl; add the vinegar, brown sugar and molasses. Cover and refrigerate.
On six metal or soaked wooden skewers, alternately thread chicken, green peppers and onion. Brush with oil; sprinkle salt and pepper. Grill uncovered, over medium heat for 10-16 minutes or until chicken is no longer pink, turning occasionally.
Unskewer chicken and vegetables into a large bowl; add 1/2 cup chipotle-molasses mixture and toss to coat. Keep warm.
Grill tortillas, uncovered, over medium heat for 45-55 seconds on each side or until warmed. Top with chicken mixture, tomatoes, cheese and remaining chipotle-molasses mixture.