I built this machine to serve as my media library server for Dropbox and Plex
Nice. Is there only room for one 3.5 HDD?
Yes. The only storage space they made available is behind the motherboard with CM's MasterBox Q300L MicroATX case. One for a 3.5" HDD and two for 2.5" SSD or HDD. You could get creative, maybe use adhesive velcro staps and attached them to the HDD between the bottom of the case. From the case it's located where one of the 120mm case fans could be at but instead use that space for another HDD.
I saw you bought two Noctua NF-F12 fans. May I ask where you installed them in the case? It seems like from the pictures, there is one fan on the front of the case as an intake fan and the other may have replaced the pre-installed fan in the Cooler Master Q300L case. Did you not use the pre-installed fan from Cooler Master or did you relocate it somewhere else in the case?
I relocated the stock fan to the top of the case above the motherboard, positioning the two Nocturas across from each other (front and back).
Even though this machine isn’t doing a ton of heavy lifting, I wanted to have all three fans just in case.