We've done a lot of work with x-cart, and created many
x-cart mods and addons, having worked with x-cart daily since 2002.
Usually with our clients we recommend:
1) Move the site to root (not in an x-cart, store, or shop directory, etc.).
2) Install our CDSEO mod (
http://www.websitecm.com/x-cart-mods...seo-links.html) for optimum spidering.
3) Requesting a robots.txt from us for use with CDSEO to prevent duplicate content.
4) Put this line in .htaccess to prevent the redirects that x-cart inately uses.
DirectoryIndex home.php index.html index.php index.htm
5) Redirect your old pages to your new CDSEO pages so that your links are not lost/broken.
If your interested in more information, I'd be happy to speak with you, just contact us.