The ATV trails are awesome. We start out in Hill City and get a side by side for the day. They'll give you a tablet that gives your position on the trail map and tons of shit to discover. Old mines, cabins, look outs, Miners Motel which is a little cave with some old bunks in it which is a easy hike. The side by sides are licensed and can drive on the road for faster trail hopping.
For a more challenging hike, do Black Elk Peak, highest point between the Rockies and the Pyrenees mountains in France. Bring lots of water and hiking sticks as this is a moderately challenging hike. We like to start off at Sylvan Lake. Take trail #9 up and Trail and trail #4 back. You'll probably want 7-10 bottles of water/person and maybe a snack. Hike and views are pretty badass. Sylvan Lake has a very nice and easy trail going around it that's worth the time to do it as a warm up or cool down.

Custer State Park is awesome, as is Wind Cave.
Iron Mountain Rd and Needles Highway when you do your Rushmore visit. Get out at the tunnels, some of them frame Mt. Rushmore and you may miss it if you're going the wrong way.
I typically avoid Deadwood and drive around the tourist strips in other towns. Seen one you've seen them all. Good stops for ice cream. Art galleries are sometimes neat with local stuff.
If you check the other thread in the SD forum "hidden food gems" it has few restaurant favorites in the west half of the state.
There will be an abnormal amount of motorcycles on the road, so watch for them.