Preheat oven to 325°F.
Scrub the ham well with a stiff brush under running water, position it on a rack in a large baking pan, add the water, cover, and bake for 2 1/2 hours, adding a little more water if necessary.
Meanwhile, combine the bourbon and apple juice in a saucepan and boil over moderately high heat till reduced to about 1/2 cup. In a bowl, combine the brown sugar, pecans, honey, and cayenne and stir till well bended. Add the bourbon mixture and stir to form a paste.
Remove the ham from the oven and increase the heat to 400°F. Remove and discard the skin and all but about 1/2 inch of fat, score the surface in diamonds, and rub the paste evenly over the top and sides. Return the ham to the oven and bake, uncovered, till the surface has a glossy mahogany glaze, about 30 minutes.
To serve, let the ham stand out for about 30 minutes on a platter before carving into thin slices.
Learn more about James Villas' cookbook Pig: King of the Southern Table by reading Nadia Arumugam's book review from the June/July 2010 issue of Fine Cooking.