I am not surprised that you've ended up with the CreateFile error after doing that.
As general advice, manually creating/modifying the directories within C:\Certbot isn't a good idea because Certbot creates them with specific directory ACLs on Windows. Those ACLs are lost if you create those directories by hand.
I'm not sure whether there's a great way to fix the directory permissions if you've modified them in any significant way, other than starting from scratch with a new C:\Certbot directory.
Unfortunately, the rate limit error you're currently experiencing won't go away until a week has elapsed, even if you do that.