Modification to the category and post template logic to behave like pages (selectable through admin)
Not currently. With the custom post types functionality in 3.0, the purpose that I had in creating ICE has been solved through core code. I suggest you look at http://wordpress.org/extend/plugins/simple-custom-post-type-archives/ if you are wanting similar functionality through 3.0.
Did you upgrade your theme? Selections from the manage > categories panel are stored based on theme directory and version.
Visit the plugin homepage - idealienstudios.com/projects/ICE/