tar.bz your /home directory and save it to a CD (or across multiple CD's) If you have stuff stored in /root, you'll want to back that up too. In general, you shouldn't be using root nearly that much.
Reinstall FC4 from scratch.
(It is worth taking some time to re-organise your partition scheme, now, so you will have less painful upgrades in future. The object is stick the parts of the tree you would store your modifications in, into their own partitions. Next install, those partitions get left alone.)
When you get to partitioning - remove all linux partitions and start over.
Do not use the default scheme
Make a seperate partition for boot, swap, and root, as normal. Also create partitions for /usr and /home.
Complete the installation.
(Check out www.mjmwired.net
for optimising the FC4 installation)
Now - /usr will contain third party software. This partition needs to be big.
/home will contain all your users and user specific stuff. If there are only one or two it may not need to be all that big.
If you have a lot of ram, then swap need only be very small - and you can actually improve performance by disabling the swap partition in fstab later (Anaconda keeps stuffing up the fstab swap entry anyway).
the root partition then need not be much bigger than the distro packages - 6-10Gig is usually plenty - since all the business goes in usr and home.
With this partition scheme. When you do your next upgrade (FC5 anyone?), you just do a fresh install again, only tell disk druid to leave the /home and /usr partitions alone. Thus saving all your data and settings.
Note: FYI: Fedora Core is a pretty geeky distro so far. Red Hat put a lot of experimental stuff in there for you to try out. You're already well on yur way in the learning curve, so I doubt you will benifit from a distro change.
Hopefully the "upgrade" issues will resolved in FC5 ... but I doubt it. They exist due to the assumption that you use only approved Fedora Project sources and you don't fiddle around. Nor do you install any binary/proprietary drivers.