Make sure that you alwas create the directory /root/ispconfig before you try the update again or you might loose the server configuration.
I seen the mysql header file issue and loaded it. Because I ran this so many times, my ispconfig directory deleted everything. Now I don't have SSL certificates, and it is not asking me to create any. I need to know how to create new ones.
I created the new certs using the post at http://www.howtoforge.com/forums/showthread.php?t=121 before I read your update. The funny thing is, I only need to get to see this configuration to help me with a clean install that will be replacing this one. Thank you for your help. I am up and running..... untl I mess it up again