If you are looking for a numerical reference point you could use the armor value of the vehicle as the base difficulty for a saber to cut through it. Not that it would always be perfect but it could work.

Didn't read through it all, but this would have been my suggestion.

If you are talking about stabbing it in and holding the blade in there like Qui-gon in Phantom menace. I would treat it as a Continuous attack. No roll is needed as it is a static target.

It would do x2 Base damage against the target every round.

Each time it Exceeded the the amount needed to "penetrate" the armor, it would equal cutting through a Few inches. To get the whole thing open would take a lot of time. (as it seemed it was taking Qui-Gon. )

As others have said, damage and armor is really only useful if the character is actually trying to destroy a vehicle with a lightsaber.

Skill checks in general are really only important if either there is a chance of failure or you need to measure the degree of success. If a character is unopposed with no time constraints or other pressures, don't even roll. At that point the character is either capable of the task or he isn't.

In this case, I think the way you handled it was entirely appropriate. I probably would have considered the lightsaber a tool to provide a boost to another check or allow a check that otherwise would be impossible. Failure could have represented a number of things depending on the situation. If this was taking place during combat, failure might be penalty enough since that's a turn spent not engaging the enemy while taking fire, no different than failing at an attack check. Given the train's speed, you could decide that failure requires a check to avoid falling off, although you might also save that for a Despair. Failure could mean the character accidentally cut into components he did not intend to, although that seems more appropriate for Threat (accidentally cutting the controls to get into the next car or triggering an alarm) or Despair (cutting something critical that stops or derails the train).