Looking at
http://dev.mysql.com/downloads/mysql/4.1.html. there seem to be plenty of pre-packaged versions for the assorted glibc versions, etc., so as there's no data to migrate I'd get rid of v3 and try installing a new version.
http://www.rpmfind.net also lists lots of MySQL rpms.
As for tips, i've never used Fedora, but I'd usually look at it in reverse - if running a certain application was important, i'd pick a Linux flavour that it was supported and tested on, rather than pick the Linux flavour first and then trying to install the application.