Are there any positive parenting classes near to where you are? What does her therapist suggest?

I understand you've been dropped in the deep end but a lot of your posts seem to be concerned with discipline and punishment. All kids need boundaries to feel secure, but this one has been through so much, I think kindness and empathy are so important right now, rather than strictness or trying to reign her in. Have you tried 'time in's', rather than time outs? It's where you sit with her and talk about how she feels. Whiny behaviour is a reflection on how she feels inside, so by talking to her, she maybe able to open up more.

I really don't like time outs, they can isolate a child who is already struggling with their feelings and don't offer support.

I also think illness in any child is a good excuse to be more lenient - being ill is horrible (I'm the worst moaner I know!) but being in hospital for malnourishment & abuse must be truly awful.

Hope things are easier, good luck.