Is there any way to run php-scripts to run with their client's permissions... I know suPHP does that but unfortunately that doesn't allow me to add php_flag's and values. Thanks in advance.
You acn either use suphp or cgi-php + suexec or fcgi-php + suexec. But none of them allows the use of php_flags as php flags is a feature of mod_php only. But in suphp you can define a specific php.ini file to have site specific settings. See suphp documentation for details.