Well, it seems that was part of the issue. The SSD was from my dad, so it already had an old partition on it, which I had left in place, and formatted the free partition (the small one was 26MB). I deleted the old partition and reformatted the drive. I had an upgrade install of win10 on my old HD, and trying to boot off it would give me an error saying boot manager was missing.
So I unplugged my primary HD and backup HD and installed off the USB to my SSD. That seemed to turn the trick. Not sure why, and it was sunday so I feel like I forgot a crucial detail or something, but the system is up with a clean install. I still haven't hooked up my old HDs yet, so porting those in may be a bear but we'll see.
Thanks to everyone for the help, it was frustrating but it worked and now my system feels snappy as hell.