I sort of fixed it. I went in a commented out the SSL lines in the apache2/sites-available/ vhosts file for the domain I was working on. After an apache restart I was able to get back into ISPConfig 3 and deleted the certificate that was there, and unchecked SSL for the site. The problem now is I must have changed something without knowing. I can't get to my site at all, but I can get to ISPConfig, and there's no entry in the error log when I try to see my site. An apache restart gives:
_default_ VirtualHost overlap on port 80, the first has precedence
then it starts. I found the error that fixes this by adding the *:80 back that I must have removed by accident.
I still need to add the certificate that started all this, but I don't want to make the same mistakes. Is there any step by steps to doing the certs in ISPC3? I just checked the SSL page, and it still shows something in the 'SSL Certificate' and 'SSL Request' boxes.