Preheat oven to 375.
Place diced onions and peppers onto a baking tray and spray with olive oil, season with salt and pepper.
Place peppers and onions in the oven for about 20-25 minutes to cook through, until soft and roasted.
Add chicken, half can of green chiles, half can of enchilada sauce, can of tomatoes, roasted peppers and onions, salt, pepper, cayenne, chili powder, and onion powder to a crock pot. Mix well.
Cook on high for 3-4 hours or low for 6-7. Plan accordingly. If it is done sooner than later, it will keep.
When the chicken is close to being done (20 - 30 min out) place cottage cheese, cream cheese, cheddar cheese, milk, other half can of enchilada sauce and green chiles in a pot.
Over medium heat bring everything together. Add salt, pepper, hot sauce, garlic powder, and cayenne to taste.
When everything has come together as much as it can, you will need to either blend it in a blender or food processor, or if you have one, use an immersion blender until everything is smooth.
Boil water and cook shells until about half done, or half the time specified for the noodles.
Drain water and combine with the chicken in the crockpot. Mix in cheese sauce. This is where I would drain some liquid from the chicken if it is looking too watery. You can always add some or all of it back in later, but you will need enough for the noodles.
Cook everything for an additional 20-25 minutes until everything is incorporated and noodles are done cooking.
