Well when reviewing the list you provided, here are my comments, and they are with respect to the tasks you said you will be performing...
All the components are fine for this build. The RAM is not on the Supermicro site as being compatible however the Crucial site states it is. The CPU is fine for what you has asked it to do, it will run Plex just fine, but don't let me talk you out of buying something a bit faster, you may change how you want to use FreeNAS and enjoy a little more horsepower later on. I can't speak to the UPS, I have personally preferred APC, except the 550VA is a bit low for my taste, I prefer 1000VA or higher to allow for short 30 minute power drops. But 550VA should allow your system to shut down once a power drop occurs. If you have periodic power interruptions, get a higher VA value.
When you install your hard drives into your case, separate them evenly so you have a drive at top, empty drive bay, drive 2, empty drive bay, etc... This will reduce the drives in the center remain cooler than they would if packed together. Also, I believe that case can handle one more 120mm fan in the front, buy a good quality silent type fan to stick in there to allow good flow air flow, or you could just relocate the rear fan and move it to the front of the case. The positive air pressure will force the air out the top and rear of the case.
The hard drives and configuration are fine for what you are desiring to use this system for. I too have the same capacity but just in six 2TB drives and my system never gets above 5TB of storage, most of that in backup files because I hang on to the latest 6 months worth. and it's several computers in my home. I am toying with the idea of reducing my pool to 4 drives in the future just because my needs are modest like yours. I'm not ripping every Bluray disc I can lay my hands on, I actually rip DVDs and then only ones that I will truly watch again, and I have a few Blurays as well, just because it was purchased that way and I wanted to see if I could rip them without issue. It's nice to have bragging rights that you have a huge library on instant demand but if that library isn't being used, it's a huge waste of money.
My last comment about the boot devices... I'd go for a single small SSD (32GB to 120GB) and use that as your boot device, the bargain basement SSD will work fine. They are much more reliable than a USB flash drive and with prices being dirty cheap these days, and you not using all your SATA ports, that would be my best advice. Additionally software updates are significantly faster. A SSD will not boot your system faster over a USB Flash drive, well not faster that you would really notice it. Again, it's a reliability thing which is why I mentioned it, and not a pair of SSDs either, just one. The pair of USB flash drives is because they are not very long lasting in this environment.
Good Luck.
