Right, I found the answer at 1am!
In the vhost.conf file, you have to change all instances of any
/var/www/symlink to site
then you have to go to the root of the vhost in question and
chown -R www-data:www-data *
(assuming apache is running as that) otherwise you need to change all perms to 775 which is probably a bad thing.
Now I've got it working, the site runs like a rocket! I've gone from 5-6 seconds lag while suphp gets going on first load, to 0.17 seconds for first page load!
Of course, if I could sort out WHY suphp and any type of CGI is so slow on initial load with all the prefork settings right and loads of spare RAM, that would be better, but I've given up on that after a week and speed was the need.