sanJuan:
I see your comment on my trip report on this this site... If you didn't see it, check the link to the Google Map
http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=http:%2F%2Fhome.windstream.net%2FJHLange%2FSD_Blackhills.kml&sll=44.693064,-103.481598&sspn=0.678489,1.39389&ie=UTF8&t=p&z=9.
I only did the Northern portion, but from my trip, I would think S to N is the preferred direction.
I think the one thing to consider is how to detour the Wilderness area. I didn't ride that far south, so it wasn't an issue for me. Another thing to consider, or at least have a plan for, is what to do if you encounter buffalo on the trail.
There are a couple of guys on the Dirt Rag Magazine Forum (T-MAN and TeamFubar) who might be able to supply more local knowledge.