Clean up FocusedStackFrame layer setting.

- Putting the stack frame above the highest app window layer ends up
putting it over the IME when the caret popup is showing. This puts
the stack frame layer above the highest non-child window layer.

- Also change the timing so the layer isn't applied until all other
layers are also being applied.

Change-Id: Ic5f142998822ac1e3890a2943cda7fc86a7e7974