My site is reaching CPU limits all the time, I just ran Debug Queries and got more than 4000 queries, no wonder site is slow.
How many pages do you have? Pages.. not posts.
I'd have the same problem in the past with a site with a LOT of pages.
It's even documented as a bug.
If it is your case, try setting $use_verbose_page_rules to false in the WP_rewrite class
Edit: Class WP_Rewrite bool $use_verbose_page_rules = true Whether to write every mod_rewrite rule for WordPress pages.
since: 2.5.0 access: public
To change it, try (not tested):
Anyway, this is a hack. You should read this.
Standard permalink advice is to not start with postnames, tags, categories or authors:
From the Codex on Permalinks
I would bet my bottom $ that the permalinks are the problem, your link shows a heck of a lot wp_rewrite queries.. take a look at this a similar issue