Another interesting source of information is TerraServer. You can trace most of the Chile Line from aerial photos, practically all the way into downtown Santa Fe.
The Chile Line as an improbable railroad, and never really was a money maker, but Palmer was reluctant to give up his dream of a RR to Mexico City. After losing Raton Pass to the ATSF, he shifted his attention farther west. It took him some time, but he finally had his own rails into Santa Fe. It's almost as he was saying "So there, by gawd".
CJ