1) The one-drive patch would be part of a custom kernel (like MLord's hijack). It tells the kernel not to look for a 2nd drive, thus not having to wait for it to spin up and decreasing boot time by a couple seconds. If you're running the standard 2.0b3 kernel, this is not an issue.
2) If the problem is intermittent (sic?), then it may be a loose jumper on one of your drives. An inch of Electrical tape, placed correctly, goes a long way.
3) There are a few backup options. If you have 2 drives with enough space, you can just copy the FIDs from one drive to the other and force a rebuild of the database. If you want to backup to your PC, check out the FAQ