WP_query and pagination?

If you could tell us what you’re exactly trying to achieve, we can help you better!

<?php
$paged = get_query_var('paged') ? get_query_var('paged') : 1;
$args = array(
               'post_type' => 'question',
               'posts_per_page' => -1,
               'paged' => $paged,
               'author' => $user_id
            );
$my_query = new WP_Query($args);

if($my_query->have_posts()):
    while($my_query->have_posts()):$my_query->the_post();
        //Loop goes here...
    endwhile;
    //support for page-navi plugin, please refer readme.txt for further instructions
    if ( function_exists('wp_pagenavi') )
    {
        wp_pagenavi();
    }
    elseif ( get_next_posts_link() || get_previous_posts_link() )
    {
        ?>
        <div class="wp-navigation clearfix">
            <div class="alignleft"><?php //next_posts_link('&laquo; Older Entries'); ?></div>
            <div class="alignright"><?php //previous_posts_link('Newer Entries &raquo;'); ?></div>
        </div>
<?php } //if wp_pagenavi
endif;
?>

Check WP_Query documentation for more parameters.

Btw, query_posts also works with custom posts, as it takes all the parameters that you can pass to WP_Query.