I was able to fix my problem, and thought I'd pass on the info to whomever might be looking into the issue. It seemed mainly like directory issues.
To get the package to update "cleanly", I did 'ln -s /var/www/htdocs/twiki /var/www/htdocs/twiki/twiki'. To get the links to function correctly on the newly installed package, I did 'ln -s /var/www/cgi-bin/twiki /var/www/htdocs/twiki/bin'. I then added a ScriptAlias entry in my httpd.conf file for the newly linked directory. After that it seems to be working again...
