I'll give it a shot just to get the ball rolling. Not considering myself a Zimbra expert or anything; just someone who has been using Zimbra in production for a few months now, and tested for several months prior to that. Hopefully the true experts will fill in the blanks.
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- what directories need to be backed up
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You should backup the directory /opt/zimbra. Look at the Zimbra wiki for the info on backing up the Open Source edition.
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- how to restore should things blow up in your face
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Wipe out the "bad" Zimbra installation. Install Zimbra from scratch. Restore your data over the Zimbra install. Run the install again as an upgrade. Once again, look at the Wiki and search the forums for more info.
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- how exactly do you do the upgrade including typical configurations
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I've never done a version jump as big as what you will be doing, but I've never done anything more than download the latest version; run the install script; answer "Y" when prompted to do an upgrade. Of course since I've been in production I make sure to backup everything first, but it sounds like that's part of your plan. Maybe I've just been lucky, but I've never run into any problems with the upgrades.
Well, right off the bat it looks like you are running the FC4 packages on a FC5 machine. Not sure if that's the best thing to do, given that packages for both are available. Just in general I'm not a big fan of Fedora for servers like Zimbra because things change so often. With FC6 being the current version, and FC7 on its way you have to wonder how long Zimbra will continue to release FC4, or even FC5 packages. Also your not going to be able to find other package updates for these OS's. Personally I use CentOS. I know it is not "officially" supported by Zimbra, but the RHEL packages work just fine, and I'm pretty sure there are a lot of Zimbra installs on CentOS.
Just my 2 cents. Hope this helps, and good luck!