Wordpress Theme Modification

I need to customize the default wordpress theme to suit a custom coded script that is added to work with wordpress. The example url of this kind of theme is www.tofuhaus.com . That site is powered by wordpress but the standard themes and plugins won't work with the script. So the elements of of the default wordpress theme must be changed to suit the script.

I can provide the theme used in the site above your reference. I think the single.php, category.php, tag.php and other files would have to be changed.