Arrghh, this is so frustrating. After I had finally gotten everything to work (Samba, FTP, SSH, Torrent, giFT) over the course of a couple of days, I was happy. I changed the firewall config after that so I needed to reboot once more after committing to flashfs, just like I had done a million other times. Except this time, after rebooting, all my configurations were GONE. No dropbear, no vsftp, no samba, not even a damn /usr/local/sbin folder. Nothing. Is there any way to get my router up and running again without redoing everything?
Problem was solved by recreating the post-boot and post-firewall scripts and rebuilding them manually. The router kept mounting the HDD on /tmp/harddisk and I was unable to umount it. Once I put the mount script into the post-boot file, it successfully mounted to /opt on boot and all my installed packages were there again. From there on it was simple enough to edit my post-firewall into working order.
I think the problem was due to the giFT configs present on /usr/local/root/.giFT taking up more space than the flash was capable of, however I'm not sure as all those files are gone now. MAKE SURE THIS DOESN'T HAPPEN TO YOU!