One thing that could have contributed to the change in her behavior before the therapy is hormones. Not only are there the "normal" adolescent behavior changes, but they can also magnify the effects of all sorts of medical conditions. The good news: it's temporary. The bad news: it'll probably take a few years
A permanent condition does not mean that the presentation or ability to function will stay the same. I think that can be a distinction that many people don't realize until after they/their child have been diagnosed a while. An example that might be easier to imagine is a kid with cerebral palsy (CP). CP is permanent and your "type" of CP doesn't change, but with physical therapy and other treatments, many people with CP are able to walk and do other things they couldn't do when diagnosed.
I'm glad Savannah is happy with the changes so far. Don't feel, however, that you have to "fix" every single indicator for Asperger's. Not only are there symptoms that are neutral, but there are ones that can be very beneficial down the road. Plus, some of it is probably just personality and you don't sound like you want to change who she is. If she feels she can, I suspect she'll be able to tell you if there are things that she doesn't want to change that really aren't effecting anyone negatively. I know too many adults with autism/Aspergers who found some of the therapies they were forced through, for things that weren't causing any problems past maybe "looking different", traumatic (which isn't good in general and could end up magnifying whatever behavior is supposed to change). I suspect most of the parents involved didn't even know how their kids felt about what they were going through. Clearly what you're doing now is positive for Savannah, but it's worth keeping an eye out in case a treatment down the road doesn't help her be happy.