So you have rebuilt Apache on your cPanel server to use suPHP instead of mod_ruid2... but you are receiving 'Forbidden' or 'Internal Server Error' messages when you try to visit your sites. This is down to file/directory ownership, and rights of execution, but not to worry - it can be easily fixed by running a couple of commands via SSH.
Firstly, let's cd (change directory) to the home directory of the user you're experiencing problems with. Obviously, replace username with the real username!
cd /home/username/
Next, we are assuming that all of your website content, including any subdomains, is all stored inside public_html. With this being so, run the following command, again replacing username with the real username.
chown -R username:username public_html/
And finally, we want to give proper read, write and execute permissions to files and folders, so we want to run this command too.
find public_html/ \( -type d -exec chmod 755 {} \; \) -o \( -type f -exec chmod 644 {} \; \)
