Excellent South Dakota trip with all your suggestions. We did pretty much everything folks suggested. Highlights for us were 1) Black Hills Wild Horse Sanctuary (700 wild horses), 2) Custer National Park (buffalo "jam"), 3) Devil's Tower (before I like Close Encounter of the Third Kind; 4) Mt. Rushmore (can you name the 4 presidents - Washington, Jefferson, Lincoln, Roosevelt); 5) Crazy Horse (but what a funding mess!); 6) Bear Country (had to be a hundred bears.... but separating the cubs in from their moms in the "zoo area" was sad); 8) Mammoth Site (a sinkhole!); 9) Wall Drug (but so touristy); 10) Deadwood "street arrest" (it was raining so we missed the trial) and 11) Badlands (this would had made it higher on the list, but we were just exhausted by the time we got there!). Let me know if you want details of any of these. Definitely a worthwhile family trip!
My favorite is Spearfish Canyon. If you missed it this trip, but sure to catch it next trip. It's beautiful!