Let the ham sit at room temperature, 1 hour. Preheat the oven to 350 degrees F. Combine the butter, 1/4 cup mustard and the thyme in a mini food processor. Process until smooth.
Make 8 to 10 deep cuts in the ham, about 1/2 inch apart, diagonal to the longest side of the ham (regardless of where the bone is). Rub the butter mixture over the ham and all the way into the spaces between each cut. Insert the orange and pineapple slices into the spaces, allowing the tops to stick out.
Transfer the ham to a rack set in a large roasting pan. Pour 2 cups water into the bottom of the pan and tightly cover with foil. Roast until a thermometer inserted into the center of the ham registers 125 degrees F, 2 to 2 1/2 hours. Remove from the oven.
Transfer 1/2 cup of the pan juices to a large skillet and add the pepper jelly and the remaining 1/4 cup mustard. Simmer over medium-high heat until thickened and slightly syrupy, about 3 minutes. Pour the glaze over the ham and brush to coat the entire surface.
Return the ham to the oven and continue to bake until the surface is caramelized and a thermometer inserted into the center registers 140 degrees F, 30 to 40 minutes. Remove to a cutting board and let rest at least 15 minutes before slicing.