So, it appears, that you want to side-grade an (ITX? SFF?) gaming setup, into a full-sized ATX case / mobo for more room, cooling, and expansion (and as you note, "many, many" HDDs).
As far as the HDDs go, possibly, would it be worth-while considering a NAS unit, or a NAS build, to complement this rig? The reason I suggest that is, is that gaming rigs, are often preferred to be overclocked for maximum performance gaming, while at the same time, multiple HDDs acting as a server, you want stability and uptime. The two are basically kind of at odds with each other.
That's not to say that you can't set up multiple larger HDDs hanging off of an ATX workstation build, for Steam game storage, RAID arrays (chipset), or other such purposes. Just be aware, of issues relating to storage and storage sub-systems, when you choose to overclock your rig for gaming (only IF you overclock).
Also, be aware, that as far as case selection goes, having a case with many intake or exhaust fans or a top port for a radiator, may not have the most 3.5" HDD bays, and vice-versa.
I built an unRAID server, in a NZXT Source 310, I think it was? It was a diminutive ATX case, with 8 3.5" HDD bays in front, and maybe a fan or two in front of them. (Fairly important, if you're going to be stacking 7200RPM HDDs on top of each other.)
I don't use it much, it was a pain to swap out drives. (Had some software issues understanding how to do so with unRAID after getting the initial disk configuration "registered" with the OS.)
I use my (multiple) 4-bay NAS units quite a bit more. I'm considering moving up to an 8-bay or 10-bay NAS. They are so convenient, quiet, and relatively low-power, compared to a build-your-own server. They are also, at the higher-drive-count end, quite a bit more expensive, and slightly more limited. (They often run a Linux derivative, with a proprietary web GUI, and "apps". The TerraMaster NAS units, which I have not used, I've heard that their default NAS OS is somewhat lacking in features, but it's on a USB stick internally, and can be swapped out for an open-source Synology derivative, or possibly, even "raw" Linux. I use QNAP, which is more full-featured, but far less flexible as far as open-source OS replacements - basically none that I am aware of. They do have a decent selection of apps, and support docker and KVM, on x64 platforms.)
It's also possible to build a "Gaming PC in a VM", using higher-end gear for an unRAID (6+) server, using KVM, and a hardware platform that fully supports IOMMU and GPU virtualization/pass-thru (I am aware those aren't quite the same thing), that would allow you to install a Windows OS for gaming, in a VM, and still have direct access to the GPU and whatnot for gaming. (Check the unraid forums for more details?)