Last time I drove this route, I-90 to Minnesota and then south thru Lake Okoboji and to my destination, Storm Lake, I went south at Moorcroft and then to Custer and from there thru the Black Hills. Then into Wall to see the Wall Drug and south thru the Badlands and back out to I-90. If you plan it right, you can do Custer state park from Custer,the pigtail bridges, the Monument and out thru Rapid City all on one route.
On Yellowstone, I would go in the north entrance from Livingston and follow the road down the westside and out the east entrance to Cody and 20-16 to Buffalo.
Coming home on I-90, you can catch the Devils Tower and the Little Bighorn Nat Monument.