Ah, the plug-in works (ish). It keeps timing out because there are so many files… It also is a pain because there are so many subdirectories since I have WordPress organizing by files by date.
Is that the only option?
@anevins, YES, thank you for the insight. It turns out the theme that I’m using is forcing WP to make the bad crops. I reactivated my old theme to reupload the image and that fixed it. Kind of a pain, but at least it works.
Thanks everyone for your thoughtful considerations.