I was able to get a few more things installed. After finishing up with SWIG and the ruby bindings so I could get Collaboa running, things started acting funny. Turns out I was running out of space on the main volume. It was then I realized that I needed to move some directories to the /mnt volume.
I moved all the usr/local stuff directories, the /var directory and with it the MYSQL files. I then went back and uninstalled a few of the items that were already installed via YUM since it appears to dump everything into the /usr directory. Since I complied Apache 2.2 myself, everything was in /usr/local/apache2.
This also lead me to further enhancements with the autorun script. It now does a bit more than simply register the domain name with ZoneEdit. I now sync the /mnt directory with S3 and then pull it back down on boot. Therefore, I'll need to create some symbolic links so everything looks good and then restart some of the services that tried to start before my script was run.
Haven't tried a reboot yet, but it's not too difficult, it will lengthen the start up time though since it's pulling about 200M from S3.
I think I'll also be running ec2-bundle-vol possibly daily to have a hot backup ready. Not sure on this one yet.