We were in the Black Hills just a few weeks ago.
We passed on Rushmore, but Crazy Horse had an awesome museum. Do the Needles/Iron Mountain road circle tour, lots to ooh and ahhh at.
Wind Cave is very interesting, and a cool escape on a hot day. Jewel Cave not as good.
Since you have a Jeep, consider some of the back roads that few ever venture out on. Lots of great scenery.
If you have the time on the way to Yellowstone, the Devil's Tower is really impressive, and the hike around the base isn't long but gets you up close and personal with the monolith. The KOA there is pretty good, with great views of the tower.
We didn't stay in Yellowstone, but used Cody as a base. The Buffalo Bill museum there is a must-see, it is huge. They were having a major pow-wow at the museum while we were there, and that was great to see. Rodeo every night as well!
It sounds like you have a great trip planned, too bad you didn't have two months!