The lesson to be learned
First, there is a bit of explanation required. Over my years of programming, my main asset has been that I can get into "learning mode" where I follow instructions explicitly and don't worry so much about what each instruction is doing until it works and I can go back over it and figure out what the instructions had me do. This experience seems to have served to teach me that there is an inherent flaw in following instructions without thinking. In the future, while following instructions, I will try to remember to do so with caution.
How it all started
So it started with a rookie mistake. I was setting up a raspberry pi 2 with arch linux, and the instructions require you to use fdisk. What did I do? I formatted my hard drive of course. I thought originally that I had formatted my linux drive (my system was dual boot). It turns out I had formatted my base windows drive.
As if that wasn't enough
So things got wonkier from there. I recovered my linux drive's data, at which time my bios interface stopped working. My BIOS didn't stop working, as I could boot into linux, but I could not access the interface (which was configured for secure boot).
I even went old school
I recovered the windows drive in linux, but couldn't boot from it. I pulled apart the whole laptop and reset the CMOS chip and nothing changed. Just at my wits end, someone on StackExchange chat suggested I pull all the hard drives and see if the bios would show up. It didn't, but for some reason when I put the hard drives back in, the system decided to try to boot from the windows drive first instead of the linux drive. For some reason that action made the bios interface accessible again.
It fixed itself?
So I turned off secure boot, and plugged in my windows drive with the intent of making the recovery partition spit out the windows key. After several hours of fiddling, I caved and bought a new copy of windows 8. I tried one last time, calling MSI tech support to recover that key, The tech support guy suggested that I press F11 on boot (something I had read about as a way to brick your MSI, but I was in learning mode and didn't think)....which made my bios not work again. Thankfully, my machine was stuck with a boot order putting USB first. I popped in my shiny new windows install, formatted the other two SSDs and it's been working ever since.
I still can't access bios, but hey, you win some you lose some.