Thanks for the link. I did not even know that feature was in Fedora. I'll have to reinstall all of the packages I removed and use that and see if it works. I probably should restore this system to default or just setup another one to write a howto.
I believe the Linux version uses whichever version of Java comes first in your path. A little Googling reveals that you should be able to use /usr/sbin/alternatives to select your default Java implementation with something like:
alternatives --config java
BTW, you should consider writing up some notes on getting Arduino to work under Fedora on the playground. The linux page is at: http://www.arduino.cc/playground/Learning/Linux
and you could create a link to a Fedora-specific page. You can register for the playground at: http://www.arduino.cc/playground/Main/LoginForm