Maybe I'm missing something but I don't understand why you are managing the window manually if you are using storyboard files.
I think you are adding universal support to an already existing project. Because if you create a new universal app everything will be just as you needed.
You need your application:didFinishLaunchingWithOptions:
method in your app delegate like this:
- (BOOL)application:(UIApplication *)application didFinishLaunchingWithOptions:(NSDictionary *)launchOptions
{
// Override point for customization after application launch.
return YES;
}
And your target settings should look like this, notice the iPhone / iPad switch and select different storyboards for each device.