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@tiesoto i'm pretty sure you'd need to edit carcols to change the vehicle colour but I haven't looked into it. using a trainer to change vehicle colour could work if you were driving the train. All the livery changes i've done just involved me changing the logos file for the train.
@yeahhmonkey I used GIMP, OpenIV and TextureTool. If you want an image with a transparent background save as a .png (not in paint it doesn't support it) and then use the editor in OpenIV to import the textures. There are tutorials for this on the OpenIV YouTube channel - https://www.youtube.com/watch?v=KMzL4iLiTb8