Well I just started working on this again... and it turns out that what I've done doesn't really work. Someone on another forum mentioned that you can disable all mouse and keyboard interactivity to windows and disable menu items so that the window can't get focus. I haven't found a way to do this from reading the documentation... can anyone help me out?
Also... if you feel so inclined, you can vote for the suggestion here so that it might get added into AIR 2.0