If anybody is interested I modified the template to make it xhtml and 90% valid w3c code.
I modified ilovejedd's template version and added some new styles.
I still have some work to do with the book_section.tpl to make it both valid and working.
As a side note, I'm using Nginx and I'm not able to download any epub. I can't test with apache so can anybody tell me if download works if the calibre directory is not inside the web site directory (in my case my web dir is /var/www/ebook and my calibre directory is /home/calibre/Calibre).
@chaley do you use any versionning system for this project ? a github / google code / bitbucket account could be a good idea, don't you think