Preheat oven to 350°F. Place ham, cut side down, in a 13- x 9-inch baking pan. Let stand at room temperature 30 minutes.

Bring apple cider, brown sugar, butter, bourbon, mustard, vinegar, peppercorns, nutmeg, cloves, and cinnamon stick to a boil in a small saucepan over medium-high. Reduce heat to medium-low; simmer, whisking occasionally, until reduced to about 3/4 cup, about 25 minutes.

Brush cider glaze evenly over ham, allowing mixture to drip between slices. Cover pan tightly with aluminum foil; bake in preheated oven until a meat thermometer inserted into thickest portion of ham registers 95°F, about 1 hour and 30 minutes.

Uncover pan. Baste ham with drippings in bottom of pan. Continue baking, uncovered, basting every 15 minutes, until ham is glazed and beginning to brown and a meat thermometer registers 140°F, 45 minutes to 1 hour. Transfer ham to a platter; let rest 10 minutes.

Strain drippings from bottom of baking pan into a small saucepan; discard solids. Skim off the majority of fat using a spoon; discard. Bring drippings to a boil over medium. Cook, stirring occasionally, until mixture is thick enough to coat the back of a spoon, 3 to 5 minutes. Pour drippings evenly over ham; serve warm or at room temperature, garnished with small apples, if desired.