Preheat the oven to 400 degrees F.
In a large bowl, whisk together the flour, baking powder, baking soda, pepper, and salt. Add the buttermilk and butter and mix just until incorporated. Don't overmix. Add 2 cups of the Cheddar (leave the rest of the cheese out to come to room temperature) and the green onions and quickly mix to combine. Wrap in plastic wrap and chill for 15 minutes in the refrigerator.
When you are ready to bake, spray 2 baking sheets with nonstick cooking spray. Tear off pieces of dough and roll into balls about the size of a golf ball. Arrange them on the baking sheets, brush them with a little buttermilk, and bake them until golden brown, about 10 to 14 minutes.
In a stand mixer using the paddle attachment, whip the remaining room temperature cheese until it is smooth.
Slice each biscuit in half and spread a teaspoon of whipped Cheddar onto the bottom. Cut a piece of ham to fit and put it on top of the Cheddar. Dollop with 1/2 teaspoon Red Pepper Jelly and cover with the top of the biscuit. Repeat with remaining ingredients and arrange on serving platters to serve.
Red Pepper Jelly:
Add the peppers in the bowl of a food processor and process until they are coarsely chopped but not pureed. Transfer the peppers to a large pot and add the cider vinegar, sugar, salt, crushed red pepper flakes, and jalapeno. Mix well.
Put the pot over medium-high heat and bring the mixture to a boil, stirring frequently. Add the pectin and continue to cook at a slow rolling boil, stirring frequently, until the jelly drips very slowly from a metal spoon, about 20 minutes. Pour into jars, let cool, cover, and refrigerate for up to 2 weeks.