OK, I'm going to close this thread with a solution to the problem.
With Boucher reiterating "use your cocoa skills", I was able to fix
the issue.
I defined an outlet in FileOwner called "myWindow" and pointed it to
my window object. In AppController.j, I defined IBOutlet id myWindow
and was able to use it in code.
Here's the link to gist if anyone's interested.
http://gist.github.com/83641
Thanks!