What is the problem with the passenger station script? Trains will not st6op in the middle of the platform and will not load/unload passengers. The stations script is not player configurable.
Most station scripts stop the train at the end of the platform. A few have been set up to stop in the middle. It is all in the GS file of the asset, <kuid2:122285:3401:22> AJS Invisible Station 1T 3.5 can be used for stopping near the middle. Some stations can stop trains of different lengths at different points within the platform.
As far as loading and unloading, make sure the station and cars are using the same passengers. You can add passengers, that are used by the station, to the cars.
