Using custom tables for old posts

a simple and Not perfect solution which will do most of the job for you is to overwrite the table names like this:

function custom_prefix_change($sql) {
  global $wpdb,$wp;
  $prefix = $wpdb->prefix;
  if(is_single()){
      //check if the post exists in the genuine posts table
      $results = $wpdb->get_results($sql,"ARRAY_A");

      if($results[0]['ID']){
          //if exists then return
          return $sql;
      }else{
          //else change the query
          $sql = str_replace("$wpdb->posts","{$wpdb->prefix}custom_posts",$sql);
          $wpdb->term_relationships = $wpdb->prefix . 'custom_term_relationships';
          $wpdb->postmeta = $wpdb->prefix . 'custom_postmeta';
      }
  }
  return $sql;
}

Now for a complete solution you will need to replace the tables in the terms_clauses filter hook for get_terms and get the meta data from the custom table yourself using the get_post_metadata for get_post_meta.