Just some thoughts on the D&S. the Alamosa and Silver Vista are "adult cars" where each ticket holder has to be 21 years or older. Right now, and for the rest of the summer, we will be running the San Juan. It is an original closed vestibule car, and also includes historic narration along the way. That is if you are looking for something inside. As for the open air gondolas, if you come prepared with layered clothing then the weather shouldn't be a major problem. Of course, if it rains then you will get a bit wet, but our gondolas do have roofs overhead. I always tell our passengers if you are going to plan around the weather you will drive yourself crazy. I highly reccomend choosing an open air gondola, the views are spectacular, the seats are comfortable and you'll be able to enjoy the sounds.
Also, I highly reccomend ridding the train in both directions, unless a nine hour day would be too long. If you choose round trip, it doesn't matter what side of the train you sit on because we turn the whole train around in Silverton for the return trip. Both sides get both views.
As for Chama, I completely agree that taking the bus to Antonito and the train back is the best way to go. Also... the turkey dinner is the best!!!
Have fun!!! Look forward to seeing you in Durango.