I have responded to your ticket but I wanted to update the thread here in case any others found this.
The problems seem to be related to edits of the menu.php file for the menu. The duplicate products listed in the main level of the menu are due to a missing WHERE clause that is present in the default menu.php file.
WHERE CategoryParent = 0
The links to the details page that are coming up as 404 are going to the wrong page, the page they should be going to are <a href="<?php echo($assumedRoot); ?>Products_Results.php?Search=1&ProductCategoryID=<?php echo $row_menuwriter_categories["CategoryID"]; ?>">