Preheat oven to 425 degrees.
Slice jalapeños lengthwise. Use a spoon to remove seeds and membranes from peppers.
Mix cream cheese, sharp cheddar cheese, and diced shallots. Fill the hollowed-out peppers with cream cheese mixture.
Place the sausage on top of the cream cheese. Wrap the half slice of bacon around jalapeño and secure with toothpick.
Place in 425 degree oven until bacon is crispy. 20-25 minutes.
Alternatively these can be cooked on the grill. Cook on a medium heat grill until the jalapeño is tender and the bacon is crispy. Keep lid closed while grilling.