FWIW,
I tried the automatic scripting and it also failed. There were errors with the db. That’s when I decided to do it manually as I have done many, many times before. I see that when I do things in the various virtual servers that I should change to that user using the su command. I noticed that when I updated to Drupal 7.2 that when I ran cp -rf drupal-7.20/* public_html/ as me that it prompted me at each file. So I switched to honor and the same command ran with absolutely no prompts as it was intended to do. I haven’t checked clean urls, but I am hoping that they are working fine. Thanks again for the help!