One would imagine stopping would be easy (hit the brake) unless the baddies sabotaged the controls. Which adds a fun element of danger (and consequence to the adventure).
If that's the case I'd start by breaking the skill challenge into 3 quick, smaller challenges: find the problem, fix the problem, stop the train. BIG complicated skill challenges tend to result in insta-failure with the three-strikes rule while many smaller challenges add-up to the same xp, have less chance of failure, and add variety.
And it segues into a good success/failure mechanic; the PCs have so many rounds/minutes before they hit the platform or reach the end of the track. Failure costs them time, success breaks even, and perfect success (no failures in the skill challenge) gains them time. It also helps stop a single PC from dominating the challenge as that takes multiple rounds, while if every PC rolls on their own it might only take one or two.
Deducing the problem: There'd be Perception checks to notice possible problem areas and broken parts (limit to the number of successes). Maybe an Insight check to figure out how goblins would sabotage the train. Streetwise and Thievery would also let someone think like a saboteur. History could even work ("I remember when the 4:10 to Yumordor was hijacked, they did X").
An Arcana check would be less useful, but could confer a bonus to figuring out the problem (and/or cancel a failure).
Fixing the problem: this could be more Arcana dominated, but you could justify it only aiding or assisting with checks. But there could be a physical component to actually moving objects and re-routing parts/power. So Athletics and Endurance come into play. You could also justify Thievery for it's manipulation of parts and undoing damage. Again, a case for History could be made ("After the crash of '79 they added emergency brakes").
As a side-note and break in the skill challenge flow, fixing the problem might be in a totally different part of the Lightning Rail. The front controls are smashed, so the PCs have to quickly get to the engineering car.
But, oh those baddies locked the doors and now time is of the essence. So the PCs have to move along the TOP of the Rail. And possibly get ambushed by another group of baddies and have a fight on the top of the moving/rocking Rail Car.
But the jumping between cars. Extra-difficult since the rocking would making moving hard (entire top difficult terrain).
Stopping the train would be dominated by Arcana. Since it had less use in the above it's a good time to let it shine. You could allow an Athletics/Endurance component to the brakes, but to differentiate and swap roles, the big physical part could only offer a bonus or cancel a failure. The defenders buy time by yanking on the emergency brake levers while the arcane types works the controls.
Alternatively:
Start at the beginning and define the terms of the challenge. What does success look like? I'm assuming they safely get the lightning rail and any remaining passengers or cargo to town.
What about failure? Stranded in the wilderness? Derailed train? Dead passengers? Lost cargo?
Possible skill uses, and the complications that drive them...
Bluff/Intimidate/Diplomacy: Convince the vehicle-bound elemental that it wants to go to town. This may be a 3.5 artifact, and not applicable anymore.
Acrobatics/Athletics: climbing out on the moving train cars to secure something or repair something.
Arcana: Diagnosing any problems with the engine/elemental.
Perception: Diagnosing any mechanical problems.
Arcana/Thievery: Fixing a relevant problem.
Heal: Keep a wounded passenger alive while the train finds it way to town.
Perception/Nature/History: Knowing which route to take if the tracks diverge, or watching the tracks ahead for obstructions.
Diplomacy/Streetwise: Keep the passengers calm (not a real success, but may provide a bonus to the next check thanks to the peace and quiet?)
Endurance: serving as a human circuitbreaker for the lightning to drive the engine.
