You can install PHPnuke without touching the shell, the installer will populate the DB for you. The trick is to set up your databases first and give them time to be enabled by DH before you run the installer.
The latest version (and security patched versions, anything after 2.9) resolve the php vs php-cgi issue, so you don't have to troubleshoot that anymore and, as far as I can tell, enabling mod_security seems to secure it pretty well.
That said, while PHPnuke has a great community its releases are riddled with security flaws and botched coding. It is not really a true opensource project but is held close by its "developer" and, IMHO, is sort of dead end at this point.
Maybe look at Mambo or Postnuke (forks of PHPnuke) or other, newer opensouce CMSs too. Try playing around at http://opensourcecms.com to try out the various options before you install anything.
Of course, if you are running a gaming or clan site, PHPnuke is your CMS
You can convert your stand alone phpBB to BBtoNuke (the portal version) with a script available at Nukecops.com or Nukeresources.com