Some menu items wont budge

The admin bar is hooked incorrectly.It should be hooked to wp_before_admin_bar_render.

This is what I use (and works):

function alter_admin_bar() {
    global $wp_admin_bar;
    $wp_admin_bar->remove_menu( 'customize' );
    $wp_admin_bar->remove_menu( 'ddw-gravityforms-toolbar' );
    $wp_admin_bar->remove_menu( 'members-new-role' );
    $wp_admin_bar->remove_menu( 'new-media' );
    $wp_admin_bar->remove_menu( 'new-post' );
    $wp_admin_bar->remove_menu( 'new-user' );
    $wp_admin_bar->remove_menu( 'wp-logo' );
}
add_action( 'wp_before_admin_bar_render', 'alter_admin_bar' );

Regarding the side menu I don’t know. My first guess would be that you’re using incorrect identifiers.