I recently went to north and south dakota and hope some of these notes help...
Custer had Prarie Dogs near the road, but you couldn't get a close up view of more than one. TRNP had a Prarie dog town hike. The trail wasn't that well marked and took longer than expected, but once we go there the walk was worth it. There were Prarie Dogs all along the trail.
TRNP had some wild horses in the north section. There were also longhorn steer as well as bison and longhorrn sheep. If you stop at the visitor center they'll tell you where they are and might even offer you binoculars to borrow (we didn't see any sheep but saw the other animals along the road). There seemed to be only one ranger in the park as when we got back return the binoculars there was a note on the door saying the visitor center was closed and he'll be back in half an hour. The North section is pretty small. We were there for 3 hours and felt like we did everything (no long hikes). There were probably 10 cars in the whole park. There are a few nice lookout points and the scenery is gorgeous.
The south section loop was closed off near the end, so you'll probably have to drive in and out.
Not sure when you're going, but the road between the north section and south section was officially closed as well. We ended up still trying and taking a detour that showed up on Google maps through dirt paved roads that saved us an hour of detour time.
I dont recall seeing any sunflower fields.
In Custer, if you do the cathedral spires hike, look out for mountain goats! We managed to meet a mom and kid along the path. We also rented kayaks on the lake there. The shop was closed for renovation so they were renting them next to the lake on first come first serve basis. Cash only if I recall correctly.
Not sure if it's worth it for you, but we drove out to devils tower on our way to TRNP. It wasn't too far out of the way and was a nice walk around.
Parks are $30 each, so if you do more than 2 it's worth it to buy the park pass for $80. We used it at the badlands, devils tower and TRNP and now have a year to go to more.