Fatal error: Maximum execution time of 30 seconds exceeded in /home/so

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My Joomla 2.5 site was hacked. All of the root files were deleted. With help from Nick W in Tech Support, we got the index page to load. But, clicking on any menu items returns the following error:
Fatal error: Maximum execution time of 30 seconds exceeded in /home/southa13/public_html/libraries/joomla/html/html.php on line 214

sometimes the line number will be 222 or a different line number.
I have reloaded the core Joomla files for the latest version.

I have added a new .htacces file and a new php.ini.

Hello Charley, and thanks for your question. The PHP error that you are encountering is caused when a PHP script takes longer to execute then the server allows for in the php.ini file on the server. It can occur like you've seen, at different lines in your scripts, because it could be getting held up at different points each time. We have a guide on how to fix a Joomla hack and upgrade for security which might offer some help into this problem. It unfortunately looks like something has occurred in your Joomla files which is causing them to seemingly loop and hang when a sub section of your site is pulled up. I also noticed that you've had over 89,000 requests today from the User-Agent SiteLockSpider as they seem to be scanning your site and keep hitting non existent URLs. If this is an external scan that you started, you might wish to have it stopped until your issues with Joomla are resolved. - Jacob