I've somehow messed up my FX Factory Pro and the apps uninstaller simply hangs. So I followed Walter Soya's awesome suggestion for someone else:
"Look in Macintosh HD > Library > Application Support > Adobe > Common > Plug-ins > (pick your version of AE) > MediaCore, and you should find two files for FxFactory: FxFactory.plugin and ImporterFxFactory.bundle. - Walter Soya (Creative Cow)"
Now AE opens right up without warnings. Awesome. However, the FX Factory plugins are still present in the Effects panel. They don't work, but are there.
Is there a way to manually remove those also? FX Factory's plugins aren't easily identifiable in the Application's plugins folder, so I don't know how to do this.