I would suggest crate training also. It won't stop her whining or barking, but it will keep your apartment from being destroyed, and will keep her out of danger.
Aly's suggestions are great, that's everything I have read about separation anxiety--I think the most important one is making your entrances and exits low-key--as hard as it is, you have to ignore her for a while. Putting her in a crate or pen is not punishment, it's for her safety, hopefully she will soon see it as her "den", and enjoy it.