My favorites. Hmmmm. I like the Sturgis trail system. Probably has the most miles of any single system in the black hills. A HS friend of mine is the head guy in charge of them. That said, if you stay west of I90 it's much better. East can get sandy in spots, hike a bike sandy. That said if you know where to cut off at several road crossings you can skip most of the sand. They also connect
with the Centennial trail so once you hit that you can head south to your heart's content and just turn around and come back. We usually start at the "campground" and start up bulldog...It's also fun coming down. If you do want to ride the east side, start at lion's club park.
Hansen Larson in downtown Rapid City is fun. Urban trails but pure xc.
I like Tinton(offically two bridges I believe), up and down in spearfish. Big hill trailhead puts you at the top of tinton. It's a cool almost 7 mile long segment, mostly downhill from that trailhead. You can climb up from town too. It's a long slog, but used to separate the wheat from the chaff during the Dakota 5-O 50 mile race.
Also, Storm Mountain, which is a bit closer to Custer, right by Rockerville, is fun. My brother used to live just off the Victoria lake loop trails by Rapid City which are not bad either. Obviously that used to be his go-to ride.
All of these trails involve significant climbing (and descending) but sounds like that is not foreign to you. You definitely earn the miles.
FWIW the Mickleson is an old railroad grade. It's fun. 109 miles North to South. Lots of great scenery, tunnels, railroad bridges, etc... We did it in a single day my one and only time riding it. It was my first century. If you just need a training ride, it is decent for that, and it does go through most of the hills towns.