Preheat oven to 350 degrees F. Score the ham with a cross hatch pattern through the thick layer of skin and fat. Arrange the onions in the center of a foil lined sheet pan large roasting pan and set the ham on top of them. Bake for 1 hour.
Meanwhile, stir together the apricot jelly, water, thyme leaves, mustard, 3 tablespoons of the vinegar, the molasses, worcestershire, allspice, and cloves in a saucepan. Whisk over medium heat until the jelly has dissolved and sauce is smooth, about 4 minutes. After the ham has been baked for 1 hour, brush with the apricot mixture every 15 minutes for another 45 minutes or until nicely glazed. Transfer the ham to a serving platter, tent with foil and set aside while making the sauce.
Discard the onions, remove foil and pour the sauce into a skillet. Add the broth and bring to a boil over high heat. In a small bowl, mix the butter and flour together until you form a paste. Whisk into the pan juices and let sauce simmer until thickened like gravy. Finish with the remaining tablespoon of vinegar and season with salt and pepper to taste.
Thinly slice the ham and serve with the sauce.
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