Multiple custom post type loops in category.php

Solution:

//make sure these custom post types are registered for taxonomy queries

add_filter('pre_get_posts', 'query_post_type');
function query_post_type($query) {
  if(is_category() || is_tag()) {
    $post_type = get_query_var('post_type');
    if($post_type)
        $post_type = $post_type;
    else
        $post_type = array('nav_menu_item', 'venue', 'story'); // don't forget nav_menu_item to allow menus to work!
    $query->set('post_type',$post_type);
    return $query;
    }
}

was filtering the results (before? after?) the in-template query. As such, it was completely obliterating the requests to only use the requested post type. Changed to

//make sure these custom post types are registered for taxonomy queries

add_filter('pre_get_posts', 'query_post_type');
function query_post_type($query) {
  if( is_tag() ) {
    $post_type = get_query_var('post_type');
    if($post_type)
        $post_type = $post_type;
    else
        $post_type = array('nav_menu_item', 'venue', 'story'); // don't forget nav_menu_item to allow menus to work!
    $query->set('post_type',$post_type);
    return $query;
    }
}

And then on-page custom queries started working.