Prepare a smoker according to the manufacturer's directions, using the wood chunks and achieving a steady temperature of 275 to 300 degrees F. Place the chiles directly on the smoker rack (or use a shallow disposable foil pan) at the cooler end of the smoking chamber or on the upper rack if your smoker has one. Lower the cover and smoke the chiles for 2 1/2 hours, or until they are soft, brown, and slightly shriveled. Remove the chipotles from the smoker. In a medium nonreactive saucepan, combine them with the chile puree, water, tomato paste, vinegar, brown sugar, garlic, and salt. Set over medium heat and bring to a simmer. Cook, stirring once or twice, until the sauce temperature. Transfer the chipotles to a covered storage container and refrigerate for at least 24 hours before using. They can be refrigerated for up to 2 weeks or frozen for up to 2 months. Dried Chipotles Only
After removing the chiles from the smoker, place them on a rack and leave them, loosely covered, at room temperature, until crisp, light, and dry, 1 to 2 weeks, depending on the humidity. Store airtight at room temperature.