I believe part of what the writers were going for initially was that the "bad guys" had reasons for you to root for them, and the "good guys" all have reasons for you to dislike them. Blurring the lines, as it were.
how much data are you looking to store? A usb connected mirrored pair/raid1 of 4tb drives is reasonably cheap, and could back up a faster array of smaller drives in a tb case pretty easily
I'd personally leave the original drive where it is and put the SSD in the optical bay. That way you're touching as little of the hardware as possible. Then migrate to the new drive with migration assistant.