Place chipotle peppers, brown sugar, pineapple, nutmeg, ginger, and bourbon whiskey in a blender and blend until smooth.
Use a sharp knife to make diagonal cuts in the ham about 1 inch apart and 1/2 inch deep in a diamond pattern. Place smoked ham in a large bowl; pour the chipotle marinade over the ham and refrigerate ham in marinade for 3 to 6 hours, turning ham occasionally in the marinade to flavor all sides.
Preheat oven to 375 degrees F (190 degrees C).
Remove ham from marinade, reserving the marinade; place ham into a roasting pan.
Roast in the preheated oven for 30 minutes.
Bring the marinade to a boil in a saucepan over medium heat. Whisk cornstarch and water together in a small bowl until smooth; whisk the mixture into the hot marinade. Reduce heat to low and simmer until thickened, about 5 minutes.
After ham has baked for 30 minutes, spoon the hot marinade over the ham.
Return ham to oven and continue baking until glaze is baked onto the ham and an instant-read thermometer inserted into the thickest part of the ham, not touching bone, reads at least 145 degrees F (65 degrees C), about 1 1/2 more hours. Baste ham with the glaze every 30 minutes.