In my opinion:
1. Fluttershy is more into being an earth pony than a pegasus. That's why she lives on the ground. and would rather walk than fly. so there could be some stamina there. not RD stamina, but some stamina. though I don't know how she could keep up with RD. Maybe if we factor in Flutter's inner strength? Maybe not though
2. Applejack carriage was more bigger and possibly heavier. could easily weigh more than 4 maybe 5 ponies.
I got nothing. I don't even know how they could fly over the train