From my Plugin Settings Page use check boxes to load specific css files (e.g. Bootstrap / Foundation)

You will have to create a settings page on which you will have to register your settings. Unfortunately this is no easy task, but it has been very well documented on tutsplus. Once you have implemented the settings api, you can check for the options that have been set with your settings page. Depending on the values of the options that have been specified, you would then include links to the script/css files. This should be done in the footer for scripts, so use the wp_footer action for that and in the header for css, so use the wp_header action for that:

add_action( 'wp_footer', 'wpse_include_custom_scripts' );

function wpse_include_custom_scripts(){

    $scripts = get_option( 'scripts' );

    $bootstrap = $scripts['bootstrap'];

    if ( $bootstrap ) {
        // add script tag for bootstrap js
    }

}

add_action('wp_head', 'wpse_include_custom_css');

function wpse_include_custom_css(){

    $scripts = get_option( 'styles' );

    $bootstrap = $scripts['bootstrap'];

    if ( $bootstrap ) {
        // add link to bootstrap css
    }

}

I don’t think it’s necessary to exclude bootstrap on any page though, if you are using it. The footprint of the minified css and the js are only 30kB.

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