Thanks for the info Roy. I think I will reload this on a 200GB drive that is non-raid so I can upgrade easier later and reinstall if needed. Can you please post the steps to backup the database? I'll do that prior to adding any media.
Also, I am going to have two other sets of disks mirrored, so I'll have /dev/md0 and /dev/md1. How do I stop these from showing up in the database? I only want a few folders I pick, and I will manually add the symlinks. On my current install the raid partitions are discovered, then a symlink is added under /home/public/data/other, so all the content on both partitions was added to the database, which is probably which caused all these issues in the first place.