1. Your USB suggestion worked! I went to Power Options > Edit plan settings > Change advanced power settings > USB settings > USB selective suspend setting. Changed it from "enabled" to "disabled," plugged my external hdd in, and immediately, the led came on, it started to spin, and was then detected and Autoplay came up! I am so happy!
2. As for the internal hdd, I haven't opened up my computer for the past day or so, so I can't tell you if it's not plugged in all the way or not. But, I formatted the hdd and deleted the volume AFTER it wasn't detected by the BIOS. I have yet to add a volume to the not-allocated space. So I'll probably do that with gparted on my old computer and see if that works.
Update: So I formatted my second internal hdd with gparted on my old computer. Plugged it into my new computer, and was immediately detected in the BIOS. Everything is essentially "back to normal before I built a new computer."