[Plugin: Debug Queries] Need some help reading the mySQL query output

I installed http://wordpress.org/extend/plugins/debug-queries/. I can now see which queries are causing the load on my site, but how do I trace them back to the WordPress plugin, custom page, widget, etc?

Here’s a few from my home page that take the most time based on the number in Time:

Time: 6.38961791992E-5
Query: SELECT post_id, meta_key, meta_value FROM wp_postmeta WHERE post_id IN (4654)
C

Time: 7.70092010498E-5
Query: SELECT <code>post_parent</code> FROM wp_posts WHERE ID = 260 LIMIT 1
Call from: require, require_once, include, get_header, locate_template, load_template, require_once, wp_head, do_action, call_user_func_array, adjacent_posts_rel_link_wp_head, adj

Time: 8.48770141602E-5
Query: SELECT t.*, tt.*, tr.object_id FROM wp_terms AS t INNER JOIN wp_term_taxonomy AS tt ON tt.term_id = t.term_id INNER JOIN wp_term_relationships AS tr ON tr.term_taxonomy_id = tt.term_taxonomy_id WHERE tt.taxonomy IN ('category', 'post_tag', 'post_format') AND tr.object_id IN (4654) ORDER BY t.name ASC
    Call from: require, require_once, include, WP_Query->query, WP_Query->get_posts, update_post_caches, update_object_term_cache, wp_get_object_terms

Time: 8.60691070557E-5
Query: SELECT t.*, tt.* FROM wp_terms AS t INNER JOIN wp_term_taxonomy AS tt ON t.term_id = tt.term_id WHERE tt.taxonomy = 'category' AND t.term_id = 56 LIMIT 1
Call from: require, require_once, include, WP_Query->query, WP_Query->get_posts, get_term_by, get_term

Time: 9.10758972168E-5
Query: SELECT <code>post_parent</code> FROM wp_posts WHERE ID = 260 LIMIT 1
Call from: require, require_once, include, get_header, locate_template, load_template, require_once, wp_head, do_action, call_user_func_array, adjacent_posts_rel_link_wp_head, adj

Time: 9.89437103271E-5
Query: SELECT <code>post_parent</code> FROM wp_posts WHERE ID = 260 LIMIT 1
Call from: require, require_once, include, get_header, locate_template, load_template, require_once, wp_head, do_action, call_user_func_array, adjacent_posts_rel_link_wp_head, adjacent_posts_rel_link, get_adjacent_post_rel_link, get_permalink, get_post, _get_post_ancestors

There are many others, but they all have a time under 0.0
And this is at the bottom of the page:

Total query time: 0.04057s for 49 queries.
    Total num_query time: 0.921 for 51 num_queries.
    » Different values in num_query and query? - please set the constant define('SAVEQUERIES', true);in your wp-config.php
    Page generated in 0.91223s, 95.55% PHP, 4.45% MySQL

The plug in support site is not in English. I need some guidance on how to read this output.

Most of what I read on the internet and slow mySQL queries has to do with adding indexes. I understand indexes somewhat, I used to program in Microsoft Access (Windows 98 era). How does this apply to WordPress?

I have tried deactivating plugins, changing themes, etc. Nothing has made a significant difference yet.

Can custom post types affect this? I’ve added some, but have not implemented showing them on the site yet in any significant way.