this could be a .htaccess file error or you might have the suhosin error.
can you get into the backend.? If so go to the permalinks and switch to the default and see what happens.
If you can't get into the backend, FTP to the site and go to the wp-content/themes folder and rename the atahualpa folder to something else and go into it and rename index.php to indexold.php. Doing this should force WordPress to switch to the default Twenty-ten theme and your site will be back up.
Then I would manually install 3.5.3 and 3.6.4 and look at the 'Suhosin' thread
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