San Juan Express

First one would have to get or borrow the cars.
The "Durango" at Knott's has been restored to San Juan appearance except paint. The big if is whether Knott's would lease the Durango.
Even if one is able to Lease or borrow the coaches it would be unlikely that Knott's or the D&S would even want their coaches altered at all (you had mentioned the reclining seats in the coaches) other than paint.
The D&S is closest to having a San Juan train, except they don't have a baggage car. They would really have to just re-paint a few cars, a locomotive and charge an arm and a leg for a ticket (and would get it). The D&S could fake the baggage car with the scratch build baggage for "Butch and Sundance".
I doubt that a San Juan will ever run on the C&TS, although I would love it.
IF you are serious about this, why not call the D&S? I don't know who you'd talk to over there.
Kevin