The rc2.d scripts are just links to the real files, which live in /etc/init.d
You should be able to create them from the list that you posted by logging in as root and typing "ln -s /etc/init.d/xxx S_XX_xxx" in the rc2.d directory.
You will need to do this for each one.
I would be a bit worried about why they are not there though, I would have thought that a pluto script creates these and it may even pull them from the database at startup. Hopefully one of the pluto guys can be more helpful than me.