Train Mechanics

Mark out a train car boundary every 60' and deal with skill checks depending on the location and status of players as laid out below.
Define the length of a car. 60' is a good length; it's a bit shorter than most real cars, but it keeps things moving. List each car in the train and keep track of which car everyone is on.
A player can be either on the roof or on the floor of a car. Some cars only have roofs, some only have floors, some have both. Moving on the roof is more difficult, but sometimes it's the only option.
Car Types:

Engine:

Engineer's cabin is a floor and close quarters; anyone in the cabin can control the train's speed (takes effect gradually over multiple rounds). See "speed die" below for how the speed is taken into consideration. (Can climb on the roof, though anyone on the boiler will take fire damage each turn.)

First class passenger car:

(Roof and floor. Doors front and rear. Has compartments inside and a hallway down the middle; all fighting on the floor is considered close quarters: see below).

Second class passenger car:

Roof and floor. Doors front and rear. Open bench seating; not subject to close quarters (unless you want to make it crowded and PCs care about hitting bystanders).

Boxcar:

Roof and floor. Doors front, rear, and on the sides. There is also a hatch in the middle of the car, allowing roof access from inside.

Flatbed car (empty):

Floor only.

Flatbed car (loaded), bulk metal car:

Treated as roof only.

Caboose:

Roof and floor. Door in front. Players can climb up from inside to observation level and overlook the roof without taking the associated penalties. The "speed die" varies depending on how fast the train is moving. I figure 1d4 for 60 mph; use a smaller die (1d2 or 1d1) as the train accelerates and a bigger die as it slows.

Movement:

Roofs are difficult terrain and cost 10' of movement per 5' travelled. When crawling, that increases to 15'.

Jumping between cars (floor to floor) requires a DC 10 strength (athletics) check. On failure, the creature hangs off the side of the destination car.

Jumping between cars (roof to roof) requires a DC 15 strength (athletics) check. On failure, the creature hangs off the front or back of the destination car roof.

Jumping from roof to floor or floor to roof has the same DC as roof to roof, but the creature has advantage/disadvantage, respectively.

Pulling yourself up from floor to roof of the same car, or recovering from hanging off the side, requires a DC 15 strength (athletics) check.

Jumping from roof to floor requires a DC 10 dexterity (acrobatics) skill check or take 1d6 falling damage and fall prone.

Combat

Anyone in a first class car is in close quarters and takes disadvantage to hit with a two-handed weapon.

Crawling vs. crawling has disadvantage to hit.

Standing vs. crawling has advantage to hit.

Anyone on a roof, or on a floor during a round when the train jolted, has disadvantage to hit with a ranged weapon at short range and cannot hit at long range (eg. 20/60 weapon is treated as 0/20).

At the beginning of each round:

Roll the speed die.

On 1-4, the train rocks.

All standing/crawling creatures on the roof make a DC 10 dex save or fall prone. Crawling creatures have advantage on this save.

On 1, the train jolts.

All creatures on the floor make a DC 10 dex save or fall prone.

Any creature prone on the roof makes a DC 15 dex save against sliding off the edge. On failure, they hang by their hands.

Any creature hanging off of a car makes a DC 15 strength save or falls off.

Falling off the side is instant death – the number of failed saves required to get to this point can be thought of as death saves.

Falling off the front or back causes the creature to land prone on the grating between cars.

If you are not in a tunnel, roll 1d10. On 1, you enter a tunnel.

Any creature not inside a passenger car is in darkness.

Any creature on a roof must make a DC 10 dex save to duck, taking 3d10 bludgeoning damage on failure.

The only roof movement while in a tunnel is crawling.

If you are in a tunnel, roll 1d6 along with the speed die. When the 1d6 comes up higher than the speed die, the train exits the tunnel.