I went to Philmont last summer with a crew and I made the travel plans. We flew South West to Albuquerque and rented a 15 pass. van for the crew of 12 and all the gear. When you add up the train tickets to Raton and shuttle buses fees and worry about meeting someone elses schedules the extra $20 or so per person was money well spent. The other advisers and I looked at the other options as well but renting the van and leaving it in the lot made sense to us.
As for crew gear, we brought most of it with us. It is lighter than the Philmont stuff and it is familiar. Shake down offer the scouts a chance to practice with the gear before having to rely on it at Philmont. The only Philmont issued gear we took with us was the bear bags, bear bag rope, one pot, ladle, and strainer.
We were hiking locally every other weekend to get used to duration hiking with full packs. With several over nights included with the final one with a 6,000' elevation.
The scouts should be fine at Philmont because kids bounce back after a rough day but the adults do not bounce back as well. I wish I had done more cardio before we went.
You and your crew are in for an amazing adventure just remember to enjoy it and don't let the stresses get to you.
IWTGBTP