I just installed the latest version onto a 2.5 Joomla site. During installation, the product created the SEF URLs including the menu and categories in the URL. I turned off the menu and category and the new URLs that are created are the structure that I want. My problem is that I want to recreate all of the SEF URLs created earlier. Is there a way to have the component recalculate all of the existing URLs using the newly configured rules?

Hi,
Yes there is. Open JoomSEF -> Manage SEF URLs, select the URLs you want to recreate, and in the second select-box in toolbar choose the Update URLs action and click the Proceed button.
This will also automatically create 301 redirects from old URLs to new ones if the structure is changed. If you don't want them, use the Manage 301 Redirects page to remove them afterwards.