I've settled the remainder with Kuroaitou in chat. Here's the finishing blows, a little bit paraphrased, for clarity.
The missing people are still on the train somewhere. It's impossible for all observers to cover every possible space on the train during any given moment. Nothing strange about this at all.
The bathroom murders could be perpetrated by any person without an alibi. There's nothing strange about it.
The two drivers were killed through the use of a remotely activated, time triggered, or delayed effect weapon. The door to the driver cart was opened by another conductor who owned a keycard. Marcia was killed outside of the drivers cart, with the exact method and location being irrelevant. Her body was then moved into the cart later through the open door.