How should I go about restarting a custom Apache install

It's not so much your version of Apache/PHP have been reverted - it's just the wrong version is loaded.

If you have Mac OS X's Web Sharing enabled it will auto enable the version of Apache and PHP Apple provides using the LaunchDaemon org.apache.httpd.plist in /System/Library/LaunchDaemons (this will override MacPorts version). You'll want to disable this by either turning off Web Sharing in the Sharing Preference Pane or by running sudo launchctl unload -w /System/Library/LaunchDaemons/org.apache.httpd.plist.

When you installed Apache for MacPorts it installed a LaunchDaemon into /Library/LaunchDaemons which if enabled will start up the MacPorts version of Apache automatically. To enable it run sudo launchctl load -w /Library/LaunchDaemons/org.macports.apache2.plist and you're off to the races.

If you're running apachectl to restart - make sure you've selected the right version. You may need to alter your $PATH to have /opt/local/apache2/bim before /usr/sbin

As for what version of PHP is being used; on the command line this will depend on your $PATH while for Apache it's entirely in your configuration of where the libphp5 module is. (/etc/apache2/ for the built in version, /opt/local/apache2/conf for the version MacPorts installed)

Things do doublecheck:

1. File permissions

The specified path for the new document root should allow at least read access for the Apache user, which is _www by default. You probably want to chmod 755 /Users/jonathan/mirror if the file permissions are too restrictive. What are the actual file permissions on the directory and files?

2. Virtual hosts

When you enable name based virtual hosts, the document root in the main config is ignored. Instead the root for the matching hostname will be used, and if none match it will default to the first virtual host.