What about restoring from my backups?

For the most part, you'll just do the same thing in reverse:

you@box1:~$ sudo rsync -ha box2::backups/box1/usr/ /usr/ you@box1:~$ sudo rsync -ha box2::backups/box1/usr/ /var/

But you'll need to be careful with /etc. Restore it to /tmp, then reinstall your applications, then pick and choose the directories you restore carefully. Make a backup of your new installation's /etc first!

you@box1:~$ sudo rsync -ha box2::backups/box1/etc /tmp/ you@box1:~$ sudo dpkg --set-selections < /tmp/etc/dpkg*txt you@box1:~$ sudo cp -a /etc /etc.dist you@box1:~$ sudo cp -a /tmp/etc/apache2 /etc/