Troop 454 Gainesville Florida, (North Florida Council) traveled to Philmont via Amtrak in 1995. It was great, the scouts ask to take the train on any long trip. In our case we traveled to El Paso then rented cars for the visit to Carlsbad and then to PSR. Our trip was complicated because a Hurricane had knocked out power for automatic RR crossings delaying our train. I would still go by train.
The Amtrak folks were great. They let us put our coolers in the baggage compartment so we could serve up our world famous (cold cuts, fruit, ceral and cookies) meals. My college roommate brought us pizza at the Houston train station. The scouts could eat junk brought from home or purchase it at the club car. On the last evening we ate a meal in the dining car. It was out of the movies, cloth linens, great service and a real meal. I know that the youth of 8-09K remember many things from their Philmont, but the things that mention to the adults when discussing a return is the train and the fancy dinner.
Scouts had the run of the train using the buddy system. Typically they went to watch movies or play cards in the club car. An additional unanticipated form of entertainment came from the presence of teenage females. The scouts were observed to be in one of three classifications: 1. Uninterested, 2. interested but observing only and 3. full pursuit. I beleive that at least one young lady and one scout are still corresponding three years later.
As a leader the train ride was wonderful. There were no worries, no connections, just make sure you have spare AAs for your CD player, several issues of you favorite reading material and relax.