You do not have to do a clean install of the game, but reverting to vanilla Oblivion would make following the FCOM instructions simpler, probably.
FCOM Installation Guide - http://tesivpositive.animolious.com/index.php?page=guides_mod_installation&subpage=fcom_installation_guide <-- This is my unofficial guide. It is up-to-date, unless you want to use the new BSAs (kind of still being tested.) You should also
always check the opening post of the current FCOM thread for the most current Bash Tag instructions. I maintain the Bash Tag updates on my site as well, but I think they have changed recently. I will be updating the page on that site soon, but all of the latest FCOM updates are found in the thread, of course.