The train from well is a little special because it goes off into the 3D skybox.If you don't want to bother with that, setting a basic train is relatively easy :
Lay some path_tracks along your tracks : have one for your train at its starting position and another one at its ending position, that should do it at first. Then make the first path_track target the ending path_track, and vice versa. You may want to tick the "teleport to this" flag on the starting path_track.
Make a func_tracktrain out of a block covered with the nodraw texture. Set its starting position to your first path_track.
Have a prop_static (or is it dynamic ?) for every car of your train and set its parent to your func_tracktrain.
Have an entity (anything... trigger_auto ?) start your func_tracktrain.
Enjoy the mess, you'll probably need to adjust direction and position a bit.
Once you've nailed it, add a trigger_hurt with freeze damage at the front of the train and set its parent to the func_tracktrain. It will kill people instead of pushing them.
And then you'll want to add an ambient_generic for the sound of the train, and probably trigger some events like doors opening and all kind of stuff too complex to list here, but cp_well is your reference. At least I hope you can get the basics working with the advices above...