Okay, so after I asked for help on this I decided I apparently wasn't in the mood to actually deal with it any more so I didn't until just now. But fyi, I was right about the completely obvious solution.

Unplug the external harddrive. I certainly can't prove that all the other things I did didn't help the situation, but when I finally just tried out my duh solution it made it work again.

So score one for no brainer solutions that take forever to come up with.