The C&TS has been designated a National Historic Place and is therefore protected by regulations covering historic sites (which I believe are the same NPS regulations you're talking about). In addition the there are State Historic Preservation Officer (SHPO) guidelines which must be followed as well. So the historic fabric of the railroad is protected.
However the buildings, especially in Chama, are also still in use, and will require certain modern amenities - such as Ethernet wiring, routers, computers, A/C, etc. to be useful. At the same time, the historical fabric of the building is covered by those guidelines.
There are also limitations imposed by those guidelines, for example, the original depot at Cumbres has been marked by a number of concrete markers (it was located just east of the highway - not under it), as has the old turntable and water tank. Under the NPS guidelines, none of these structures could be rebuilt since they were not there when the C&TS was formed. However the well building on the hillside above the highway crossing (it's a well, not an outhouse - honest) has been completely restored to it's original design as per NPS and SHPO regulations.
As far as a long term strategic plan, the Friends have spent some time and effort on such a document, however I am not familiar enough with it to comment on what it includes.
Don