In a microwave safe bowl, microwave the onion, oil, tomato paste and red pepper flakes, about 5 minutes, stirring often.
Prep the Peppers
Cut 1/2" top off each pepper, removing the seeds and stems. Chop the tops up fine and reserve.
Assemble the Filling & Stuff the Peppers
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.
Cook in Slow Cooker
Pour 1/3 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.
Garnish and Serve
Pick up the peppers carefully with tongs, and use a slotted spoon underneath to transfer to plates.
Let them cool for 5 or so minutes and then slice in half to serve.
Serve with fresh Parmesan cheese and basil on top.