Here were the things that were wrong and that I wanted to fix

• Comments were not working
• The default WP .htaccess file wasn’t redirecting people to the correct thread, had to resort to using custom made one
• Tried to upgrade to 2.0.2, but it was saying that I was using 2.0.1.
• The link to –Previous Posts was not working

To fix the comments I deleted the spamassassin plug-in. To fix the upgrading problem I deleted all the files that come with each release of wordpress then uploaded the new files. To fix the .htaccess I tested the default one that wordpress generates on loganlindquist.com and then tried it on this site. As an added bonus to all that somewhere along the way the previous posts link started working again.