Thanks for all that additional information, along with the successful but still frustrating "resolution". I have never tried to use a DVD "bay" for a hard drive or SSD, so my experience level with that is just about non-existent. I was also thinking that the brand of drive you have was a non-Seagate one, and somewhat god forbid, a Western Digital one. But that is not the case. Seagate drives typically "play nicely" with Macs.
From what I understand, the 1TB SSD is inside the optical bay (via a caddy), and is your boot drive (or possibly a partition on it). What happens if you place that SSD inside the nomal "bay"? Does your machine work then?
As to what the cause was/is of issues having the Seagate HDD inside the "normal" bay, do you have another brand new piece of hard ware you could "place" there, like another HDD or an SSD, to see what happens?
Additionally, have you ever done any disk cleanup/maintenance/repairs, from a software perspective, on your boot partition, ie, the partition where the OS is, and where your software that you use is? You actually can do a lot of disk cleanup on your own, and there are some excellent third party products available (both free and commercial) that can help you with that.
Finally, regarding what I mean by third party software, I mean any application that one uses which is not "genuine" Apple. Some examples, with the ones I use, are Office 2016 (Outlook for my EMail, Microsoft Word and Microsoft Excel), Quicken 2017, 1Password, Onyx, Tech Tool Pro, VLC, SuperDuper! for my backups (I do not use Time Machine for that critical task), Transmission, EasyFind (I don't use Spotlight), and AppCleaner. Of course I always keep all my software up to date, and especially making sure that my third party ones are compatible with the OS I am using (I am using OS 10.12.6 like you on both of my Macs). That compatibility requirement is the reason why I have not upgraded to High Sierra, OS 10.13.x, yet, as 2 of my critical ones do not have updates available.