>>Do you have a maintenance plan to re-build indexes (de-fragment)?
>
>Only in manual, such as I just did when I went into the application, in the administration interface, and click on the specific index to generate the script.

Try setting it up as a job based on the Michelle Ufford's script or Olla's script. So, it will automatically detect problematic indexes and re-build them as needed.

BTW, I'm reading right now (finished) this blog post
http://blogs.lessthandot.com/index.php/DataMgmt/DBAdmin/sql-server-dba-tip-missing-index-dmv

and it has a link to another interesting post (even if I don't remember it) by Brad Schulz.

Take a look.