We shuttled via the Moki Dugway both ways and really enjoyed the adventure. If you have the time and the vehicles, I suggest shuttling yourself and enjoying the views from the windshield. I plan on doing the San Juan again and will always include self shuttle as part of the trip.
I haven't read any recent posts on this thread, so I apologize for repeating anything stated beforehand. The Moki Dugway is an absolutely greatly maintained dirt road. I would drag a trailer next time and not even worry about this section.
Once again, enjoy the shuttle for what it is, cool beers while driving in the deep desert with nothing but nothingness to absorb.