How can I customize the appearance of sub-menus such as Items, Status, Equip etc?

The only customisation of the builtin 'special' menus currently possible is to change textbox styles and colours (in the UI colors editor) affecting the appearance of the boxes underneath the menus, and the text, in the Global Text Strings editor. Other than this, No.

Customisation of the layout of these menus, using the new slice system, is planned for some future version.

It is possible, with a great deal of effort, to reimplement most of the functionality of these menus with scripting (using slices) and then edit the in-game menu to open these scripted menus instead of the builtin ones.