You can make it follow or nofollow, whichever you wish. To an authority site I would personally leave it as follow.
It shouldn't make much difference what theme you use, but some specialized themes do move things about a bit. If you come across a theme where CleanMe doesn't work, let me know. I'll probably have it updated to work with that theme when present.
It doesn't do a full revert - it wipes out posts, pages, comments, links and changes the permalinks. I don't think it's really suitable for using on a hacked/ruined blog and it's not something that I would add. That would be going well outside the original intent of the plugin.
But as an idea for a future plugin, that ain't half bad...
Yes, the plugin should create the recommended links category for you. If you're willing to contact me privately I can look into why it didn't do it for you. I can have the plugin updated if there are any issues.
I'm definitely late with this, but I will give the link to a very full video showing the 7 step process and I'll post it here. Give me a day or two.