There is a bunch of different options.

Many people prefer to have separate hardware for their NAS so that it will function independently of other stuff and continue to do things like critical backups etc. Check out /r/DataHoarder for storage ideas. The classic is to get a system and install ZFS. The Avoton/Rangeley atoms (which OP used) are perfect because they are very low power yet more than enough for a NAS and they are server grade hardware so you can use IPMI and ECC ram. I use an avoton atom with the onboard SATA ports for 5 drives and it is more than enough for me. I use freenas as the software which is the most popular, but here are many other options.

check out /r/selfhosted for your other stuff. In general, I have a separate system which has a bunch of VMs that boot from a small SSD. All the VMs get storage from the NAS via ISCI. I've actually been thinking of getting a single main VM of Ubuntu and then installing docker on it for my main apps. You can get a git docker and thousands of other things.

For email, check out mail-in-a-box. Note this requires some server skills, don't dry to run email as your first server, start with the easy stuff like what I talked about above. Setup a plex+sonarr if you like media, setup owncloud/seafile/other for file sync.

There are project which combine lots of stuff like sandstorm.io. With VMs, you just have to spin up a VM, install sandstorm and see if you like it. If not, just delete the VM and everything else still works with no problems.

If you really want to go all out and build a small cluster, you can use something like openstack to manage VMs across multiple hosts. You can also use something like Ceph to cluster your storage across multiple hosts. If I had OPs setup, I would run ceph on the three hosts so that I can easily add storage over time while getting good redundancy. Note that ceph is not for beginners, you should build a simpler NAS first to get experience.