One common way to handle ownership and security for a daemon is to create a 'system user' with a low uid and no shell access. Give it a home directory somewhere in /var. To be extra cautious mount its own disk partition there.

You haven't said what you're doing that needs root access, but be awfully sparing of that. If there is some part of the task that truly needs superuser access, look at sudo or similar. The suidperl extension is still not recommended. Though is has been improved in perl-5.8.4, the developers are not yet advising its use in critical applications.

Your best bet is to work user and group filesystem permissions to provide security.

I'm always a little puzzled by constraints which assume a home-rolled server will be more secure than a known and tested one like Apache httpd.