During my attempts to scp the iPhone Filesystem (page 12-13), I was receiving out of space errors. I discovered that if I did a new Sync (basically removing all my iTunes and Movies) plus an iPhone reset, I could make the scp process work.

However, iTunes now reports that 1.49GB of memory is now occupied by Other. Is this the Filesystem or did I do something wrong?

It depends on what kind of things you've put on your jailbroken phone. It may make sense to just restore to factory, which will blow away anything you might have lingering around. Or you could use du -h / to identify what exactly is taking up so much space.