In a medium saucepan combine prunes, brandy, water and cloves. Bring to a boil and then reduce the heat and simmer for 15 minutes. Strain the prunes from the liquid, set the prunes aside to cool. Strain out the cloves and reserve the liquid.
Mix Dijon mustard, honey, and lemon juice together. Set aside.
Make a hole in the pork loin by inserting a long thin knife in the middle of one end toward the center of the loin. Repeat at the other end, making an incision that runs lengthwise through the center of the loin. If needed use your fingers to make the opening 3/4 inch wide.
Stuff about 20 prunes into the incision made in the pork loin center. Place the pork loin fat side up on a shallow oven proof roasting pan. Pour 3/4 of the mustard honey mixture over the pork loin. Sprinkle about one tablespoon of the thyme leaves over the pork loin. Cover and refrigerate for about 2 hours. Bring to room temperature before roasting.
Preheat oven to 425 F. Cook for 15 minutes. Remove the pork loin from the oven and reduce temperature to 350 F. Carefully move pork loin to a plate and scatter the shallot slices and remaining prunes on the bottom of the roasting pan. Place the pork loin on top of the shallots and prunes and pour reserved brandy liquid over the pork. Roast the pork loin for another hour, basting every so often. During the last 10 minutes of cooking time, pour the remaining mustard honey mixture over the pork. Check the pork loin temperature; 140 F for slightly pink and 145 F for more well done. Rest the pork loin for 10-15 covered with foil before slicing and serving. Serve with the prune/shallot sauce.