Yeah, my fault for getting them into that directory. I was used to it from my Netscape days, so thought it was a good idea to keep it that way. Also, the normal place for the profile is hard to migrate if changing users or reinstalling the OS.
Thanks for the Mozilla Backup link, although I'm simply planning to put the new profile in my normal data partition, so it should get backed up (not that I'm backing it up that regularly, but more often than other things).