I have seen many posts with people having trouble with internal server errors on cpanel while using suPHP as the php handler.
unfortunatley people seem to be going way above and beyond what is required to troubleshoot this issue.
A simple way to fix most issues is to simply login to your cpanel/WHM server via ssh and run /scripts/chownpublichtmls
In most cases it is simply a case that you have file permissions incorrect or you have root set as the owner on many of your files.
If that does not work then you likley have other permission based issues so I suggest you ensure all your directories are set to chmod 755 and make sure all your .php files are set to chmod 644 (suPHP will not work with permissions higher than 644)
you can check the permissions in command line by running e.g. ‘stat /home/john/public_html’
Hope it helps someone