Local Omaha Investor, with 100+ wholesale deals and helping grow to 120+ units in the area over the past 4 years. I will only speak for our market but, figure most would apply elsewhere too.
Are there any red flags with these regions? - The first thing that comes to mind are foundations. As with anywhere this can be a very costly oversight. Depending on when the property was built it could have a block or red brick foundation. Avoid red brick if you can and if you must go with it, have someone experienced look at it. At least here in that pricepoint, you are limited to a SFH but, totally doable. I'd be happy to help you find one, should you decide Omaha is the market for you. I'm also happy to answer general questions just drop me a message!
Is it a mistake to consider the rural areas that are tied to these metros? - I would stick to the metro areas if planning on offloading quickly. Which being one of your first flips/investments in the area, you probably are wanting to "realize" the profit from your investment sooner than later. More buyers in the metro areas, Omaha for one is seeing a bit of a tech boom getting new Amazon, Facebook, and Google data centers.
We have been looking on craigslist and on county/city auction lists. Of course we see some on zillow, but nearly all of these properties are priced for retail. We skim Facebook Marketplace (the functionality is rough). Are there any other places we should be looking? - Yes you need to join local Facebook "Real Estate Investors of City name here". They typically have a list of cash buyers, add yourself to that list and start getting deals sent your way. You are looking for wholesalers, typically not realtors, and never market ready properties unless you have a long term buy and hold strategy in a good area that sees a good upside for growth. Again I'm happy to help explain in further detail or to put you in contact with someone I know in the midwest. I have friends in most of the markets you mentioned.
Let me know if I can help in anyway. My wife and myself can definitely relate to where you are and from what it sounds like share your ambition! If you ever visit Omaha for an explorative trip let me know and I'd be happy to show you around! Take care and I wish you the very best in your endeavors!