Plan to do Custer Wildlife loop first thing in am (early!!) or at sunset. Too hot in the middle of the day to see much.
Wall Drugs can take a few hours if you want, so be careful. Look for the T-rex animatron. There are water fountains for the kids to play in so wear water friendly shoes/clothes there
You can sign kids up for a cool dig program at mammoth site. We loved it!! I would pick Mammoth over Wind Cave any day, but I've been in a lot of caves and haven't seen a lot of mammoth bones.
Spring for the extra $$ to get Thomas Jefferson Vanilla at Mt Rushmore. Sooo Good!
SKIP the evening show in Medora (can't remember the name but "EVERYBODY" does it). It's lame and you have way too much packed into your trip already. I don't see you have planned to do that, but don't get sucked in to that.
Be prepared to let a few things go. Weather can be unpredicatable and wild. We took 9 hours to do 6 hours of driving to get to Wall SD (bad storm, accident that shut down highway)
GET GAS before you leave SD to Medora ND- there are long stretches of highway with no visible living creatures for hours. It'd take a LONG time for AAA to get to you with extra gas.