In a microwave safe bowl, microwave the onion, oil, tomato paste and red pepper flakes, about 5 minutes, stirring often.
Cut ½" top off each pepper, removing the seeds and stems. Chop the tops up fine and reserve.
In a large bowl, mash the bread with the milk and the back of a fork until combined. Mix in the onion mixture and chipped pepper tops.
Add the sausage, zucchini, Monterey Jack cheese, rice, Parmesan, and season well with salt and pepper. Mix the filling well by hand and pack into the cored peppers.
Pour ⅓ cup water into your slow cooker and arrange the stuffed peppers upright so that they will remain standing while cooking. Cover and cook about 4 to 6 hours on low, until the peppers are tender.
Pick up the peppers carefully with tongs, and use a slotted spoon underneath to transfer to plates.
Serve with fresh Parmesan cheese and basil on top.