I would not do this.
1) Nas4free (and freenas, but they hide more from their GUI) should not need you to spend a lot of time in the command line. If they are, you need to look at why. Going to Ubuntu will not fix this.
2) ZFS on Ubuntu is brand new. Yes, people say it is stable, but it is not what BSD people call stable. Not by far. I have played with it, but I have not saved anything to it I did not have somewhere else. It is simply not where ZFS on *BSD is yet, and I am not sure it every can be.
3) You mentioned Apps not starting. I am guessing you are running things in the FreeBSD jails. These are not trivial. And a storage server does not make a good VM server. If you absolutely positively must have it all on one box...
Install Ubuntu Server and KVM.
Install a Nas4free setup in a VM with hardware passthrough for all the drives.
Feel free to have your VMs mount their drives on the virtual Nas4free, just make sure you delay starting them.
This setup is very cool and elegant! And a pain to set up and manage! (And I have seen it in production!)
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