I was playing with john the ripper to see how crackable my own passwords are. It wasn't able to crack any of my 8 digit passwords in any realistic time. However now I somehow have messed up my root access. I ran:

#> unshadow /etc/passwd /etc/shadow > outputfile

and then...

#> john outputfile

However, now I've just noticed I can no longer get to root with my regular root password. Is it possible unshadow messed this up? Is there any way to fix this, or will I forever be w/o root access?

Also I noticed there are backups or something, passwd-, passwd.bak, shadow-, shadow.bak can I use these to restore the passwords w/o first having root access?

"unshadow" shouldn't have modifed any files, so I don't know how you would have "lost" root access without editing your passwd or shadow file in some other way. If you need to reset your root password, look here.

Thank you the site you gave a link to helped. I regained superuser access to my system.

Now there is another problem though, for some reason my first user account's firefox bookmarks have been repalced with root's (or maybe the default?) firefox bookmarks. Does this give a clue into what I may have done to mess myself up in the first place?

Does this sound more like I did something dumb or that I've been owned?

I'll vote for the former.
First I googled on "John the ripper" to see if there was a history of problems, like you mentioned.
Then, I copied the shadow and passwd files to another directory (using sudo), downloaded the john tarball, compiled it and the unshadow program on the copies, (as a non root user). They are still identical to the originals. However, maybe I am doing something stupid here. I'm running it without studying the source code first, as if I would notice anything!
Even though I am not running it as root, if it can crack my root password, it would be able to become root.

It may be something else you did when you where running as the root user. You may consider using 'sudo' on individual command. If you may have done something wrong, but don't know what. You can grep /var/log/messages for the word 'sudo' and get a log of the commands performed as root:
e.g.
messages:Feb 11 04:38:07 hpamd64 sudo: username : TTY=pts/3 ; PWD=/home/username/downloads/john-1.7/run ; USER=root ; COMMAND=/usr/bin/cmp shadow /etc/shadow

The files that look like backup files for group and shadow, may be produced by your system before an upgrade, or if you used a GUI tool to set the password. Look at the modification times and the contents. They may be fairly current.