I didn't get rained on while riding the trail in 2015, but a huge t-storm with hail came through Hill City while I was camping. It was a rainy spring that year. A local in Custer told me that by mid-June they had already gotten more than a month's worth of rain. There were some washout approaching Edgemont. I was able to skateboard through them. Overall though, the trail was well maintained. They really got it right with the shelters and water cisterns.
I went south, picking up the trail at Englewood. The uphill sections there and starting at Mystic were likely tougher than they would have been had I not started the day in Spearfish with the climb up the canyon and then looping around to Engelwood.