It sounds like you might have built your Sandbox from your backup. But, eject the backup drive and try using the aliases: if the backup drive isn't there, they should 'fix' themselves.

Wow, I suppose that's possible! Yuck, that would mean that I've been working for quite a while on a hybrid machine, with some documents and apps opening up from the wrong drive, without my noticing it!

Some login items are background processes that I can't tell from where they opened. I suppose I could just remove the backup drive (it's internal) and see if everything opens, or, just delete all of the login items and recreate them. Is there an easier way?

Or eject the internal drive in Disk Utility...

Won't it just remount when I reboot or log out?

When you restart, yes. But the idea is for you to fix whatever aliases you're worried about. So you should be able to eject, log out, log back in...

Update:

After working with my restored drive for a while, and still running into some weird problems, I decided to restore from a month-old SD! backup and rebuild forward.