Bike has 700c X 38C Marathon Plus tires. You think I will be OK with this tire setup?
Did nearly all of the Mickelson Trail last June: A short, paved portion north in Deadwood and then the rest south from the Englewood trailhead to the end in Edgemont. Those tires will be fine. I rode 35c Conti Top Touring II tires and was fine notwithstanding the fact that the trail was in relatively bad shape due to the seriously heavy rain fall the area experienced that month. A woman in Custer told me they were 15" above normal for that time of year.
Are you planning to do Deadwood to Hill City in one day? If so, be prepared. The only service (besides the water cisterns) south of Lead, which in only 5 miles, from Deadwood is a bar/restaurant in Rochford, and there is some climbing as rail-trails go. IIRC, there is a climb out of Deadwood. From Englewood south there is a incline of some 5 miles. There is another long incline after Mystic that fakes you out with a false summit. The relatively rough surface compared to finely crushed limestone causes you expend more energy. Bring sustenance. But don't let that dissuade you. It's a fabulous ride.
If it would fit with your itinerary, I highly recommend staying as Spearfish. The campground and municipal park there are out of this world, and they are right next to a fish hatchery and museum. From there you can climb through Spearfish Canyon and then head to Cheyenne Junction where you can head north and pick up the trail at Englewood. That's what I did. Here is the map for that day:https://ridewithgps.com/routes/8789073
In Hill City I camped at Crooked Creek. Decent place that you can access right from the trail. There is a place closer to the town center, but it doesn't look as nice.
If you are headed to Hot Springs I assume you will leave the trail at the Minnekahta trail head at U.S. 18. If so, U.S. 18 can have some traffic, but it has a wide shoulder. I circled back to Hot Springs from Edgemont via Old Rte. 18 to U.S. 18 I remember flying along on U.S. 18 with a great tailwind and finally looking up an seeing what turned out to be about a 1 mile climb over a ridge. It felt like a cold, slap in the face:https://ridewithgps.com/routes/8789349