I'm like you and try to avoid Interstates unless absolutely necessary. It is much more relaxing traveling the backroads. It's also easier to find some decent reasonably priced campgrounds that have availability last minute.
I went across 44 last year while traveling from SE Wisconsin to Custer, SD. At Jordan Junction, I chose to keep going straight and down 18 instead of jogging over and continuing on 44. This was mid Jun and while traveling through the Rosebud Reservation, I just recall it being windy extremely windy through most of it. The towns you come to in the Reservation are all pretty run down but didn't have any problems. Very minimal traffic along entire route.
Another time out there several years ago, this time on a motorcycle, I continued on 44 all the way to Interior, SD. Again very minimal traffic and very pleasant drive. Once at Interior, instead of continuing on 44, we went north into the Badlands Park. One thing at Interior, we stopped at a little gas station called Cowboys Corner. We ate there and they make different meals every day. Not a big selection but the food was very tasty.
On the trip last year, I ended up stopping at a campground right on the Missouri River for the night. It was called Snake Creek State Recreation Area. Very nice place, reasonably priced with water and electric hookups and shade. There was another campground on other side of road called Gods Country campground. It had a religious theme which wouldn't have been an issue for me but the campers were packed in like sardines and no shade. I'm glad I chose Snake Creek instead.
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