To make the glaze: In a large saucepan, combine the root beer, pepper jelly, Tabasco, cloves, cinnamon, bay leaf, orange juice and peel, and lemon peel. Bring mixture to a boil, then lower to a simmer and cook for about 30 minutes. Strain the pan contents and discard the solids. Reduce the liquid to about 1/2 cup. Refrigerate if you do this in advance.
To prepare ham: Preheat oven to 350 degrees. Place the ham on rack in a disposable aluminum pan. Cut shallow marks in a crisscross pattern across the top half of the ham. Spoon just enough of the glaze over the ham to completely wet the surface. Combine brown sugar and mustard together and pat all over the ham. Pour 1/2 cup water in the pan.
Bake the ham, spooning some of the remaining glaze over it every 15 minutes until the glaze is all used up. Try to get some glaze over all parts of the ham. Add more water to the pan when it dries up. Bake for 18 to 24 minutes per pound for a half bone-in smoked ham (5 to 7 pounds), or 15 to 18 minutes per pound for a whole bone-in smoked ham (10 to 14 pounds), or until the ham reaches an internal temperature of 140 degrees on a meat thermometer. Remove from oven and allow to rest before carving.