Inter-country car drop between Spain and Portugal is very expensive and only offered by the big-boys like Avis, Hertz etc.
Have a look at this post on my blog which may interest you:
http://barlaventostravelblog.blogspot.com/2007/09/hiring-car-in-faroportugal-and-dropping.html
Note there is no train between Faro and Seville.
Bus is the only option.
Here is a synopsis of relevant schedules: (Click on the image to enlarge!)