OK here's what I did:
I made an extra backup of my NAND on to my computer in case this tool corrupted my only good one.
I opened up Ohneschwanzenegger and select New Nand.
I clicked Existing Nand and selected my NAND
I set it to use keys and boot 1,2 from the original NAND.
I left the Bad Blocks setting alone, and set the uid.sys to Usa (my region;probably should have left it as original though)
Clicked OK, waited, then copied the NAND it made and put it on my SD.
I installed it on to my Wii, bootmii said the NAND was fine, bootmii installed, everything OK for install.
When it was done, I tried going to my System Menu, but it wouldn't even boot. Just showed the blue background of the TV as the Disc drive was turning on. So I tried launching Homebrew Channel from bootmii, but the same thing happened. I was also unable to launch apps.
Fortunately, I had my backup on my computer, got that installed and everything was working again, but of course not settings.
Should I try doing a "Content>Format"? Or does that empty the entire NAND?