transposedmessenger

Just as an FYI, the RAM rule of thumb in FreeNAS (ZFS specifically) is 8GB minimum, otherwise 1GB of RAM per 1TB of storage. You can go lower than 8GB if you're running a very small pool, but if you have a 12TB pool, you don't need 20GB of RAM - 12GB should suffice. With that in mind, the system the OP is looking at has 48GB, which is plenty.
I just setup a FreeNAS server over the last week. It certainly has it's benefits and cons. I'm running 6x 3TB HDD's in a RAIDZ1 array (Equivalent to a RAID5 array) - 18TB raw, 15TB usable, 12.5TiB formatted.
 
I've got two Jails running:
Plex and Transmission
 
The only thing FreeNAS doesn't seem to do well is acting as a VM host. You can install VirtualBox on it, but apparently without hardware virtualization support.
 
The FreeNAS 10 Beta has a Linux based virtualization mechanism running, which is supposedly set to launch in the next Stable release.
 
The only big downside I've seen so far with my setup is moving files within the Pool. If I copy files on the network share to another location on the network share, I'm limited in copy speeds to the connection of the device I'm running. I'm on WIFI 2 floors above my server, so the speeds are a bit slow. I've actually resorted to SSH-ing into the FreeNAS server so I can run the copy command "locally", which is obviously way faster.
 
Not sure exactly why that seems to be the case, but since FreeNAS doesn't have a GUI file explorer, it's kind of annoying. This may not affect other people though, or even be a problem even if it does. It could be related to my setup in some way.

I'll also recommend Pycharm, it has never let me down. Also, automate the boring stuff.

I'll also recommend Pycharm, it has never let me down. Also, automate the boring stuff.

FreeBSD is a fine choice; NAS4Free is even better  my homeserver does fine with an old i5. However, I wouldn't recommend opening your server up to the www, too many security concerns.

Github is a good place to start.

I like this build. Good parts all around and great prices

Hey, Welcome to the forums

unRaid boots from a USB stick, but you can use a small SSD to store your Plex docker, so that the HDD drives can spin down when they are not used.
I don't use plex, you should ask over in the unRaid forums or have a read there about how much cpu grunt you need.

Well since your Windows install on the SSD is fresh and your HDD contains your documents/music/photos I presume, why not just reinstall Windows on your SSD with the other drive unplugged? That way it won't get confused about which drive to boot from.
 
Once you have your Windows up and running on your SSD, power down and plug in the HDD. When you boot, make sure the SSD is the first boot option.