Well, the whole idea of a train reminded me of a certain Maplestory event, that one ship where players sat around until reaching their destination...ONLY TO BE INVADED BY PIRATES! Yeah, I'm going there.
Because piracy is more of a sea thing, we're not gonna be going with that, instead we could add some kind of rogue renegade group, members of the renegades who were fed up with being treated like complete dogshιt by the eliatopian government and have for that reason quit the resistance and have turned to a life of crime. This could be anything, ninjas, priests, whatever deadly army group you can think of. Basically, they could sometimes invade the train, which would force players to move to the furthest back of the train, which the rogues can't reach. This could be a good way to add some surprising challenge, as they SHOULD probably be strong enough to challenge level 50s and up, seeing as there is a safe spot for weaker players to run up to in case they get caught up in the attack.
The train would best be structured like a sideways nature factory, except it has no player requirement (aka you don't need 4 players), it only has the timed gates. I have done a pretty basic ms paint shape to basically give you a feel for the area.

Yeah pretty much this, also the boss at the end should be a strong rogue, same weight class as every player, but with a lot of hp and defense, and a love for grenades. Call him Commander Vitare or something, dunno. I believe something like this would be a unique diversion from the standard "big boss spawns stuff" thing we got going with lumbercore, ooze horror and eventually moony....eventually...
On drops...I dunno! I think they would drop f1s and e1s cause of their gear (guns and bombs), buuut besides that? I dunno, you guys decide, I just want some cool events, might draw a unique model for the boss grenade dude later but don't count on it.