Feel free to substitute with ground turkey, ground chicken, or a half and half combination of ground beef and ground sausage. You can also use precooked shredded chicken, just add it in around 10 minutes before the recipe is done to heat it up.
Either shredded cheddar or Mexican cheese blend both work well.
If you can't find fire-roasted tomatoes, you can substitute with a can of regular diced tomatoes or Rotel.
You can substitute the elbow macaroni noodles with your favorite pasta shape. Shells or cavatappi are never a bad idea. Gluten free pasta will also work.