@Gertjan I did however just fix it :) I stopped panicing for a second and started thinking laterally. I noticed that /cf/conf is actually a zfs filesystem. So I said zfs mount /pfSense/cf/conf and it insisted it was mounted. No conf directory there, so something amiss. I have nothing to lose at this point staring at a reinstall with a 4 month old backup. I simply unmounted it and remounted it, and I have my configuration back, the GUI is working and I have saved the current configuration to many places :)
Thanks for the suggestions, much appreciated :)