Part 1 of trying to get hacks to FreeNAS to survive an upgrade was a failure. But never fear, I went back to the drawing board and had great success tonight. Basically I changed my approach slightly, Instead of trying to make changes to /conf/base/etc/rc.conf , what ended up working was just making the changes to /etc/rc.conf on every boot.

This will have the added benefit of working even if the FreeNAS developers change their naming scheme again for things in /conf/base/etc.