Hey ADPBoss, good luck with your new site
Here a few things I have done (all these give indications as to what you might have done and what version of the store you are running):
CHMOD 000 the following files:
NOTE: You will need to CHMOD some of these back (files with *) to 644 when you upgrade to the next version.
Drop and .htaccess file with "Deny from all" in the following directories:
NOTE: some of these directories might have the restriction in place already so just double check it.
In the root directory of your web, add/modify the .htaccess file with "Options -Indexes
This way any directory that does not have an index file in it will not list the directory contents.
I think that is it for now... I'll keep adding as I come across more stuff!