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I myself emerged Firefox, which built it from the source, and after that Java worked just fine which is helped by Gentoo having Java already in it. It's usually a good idea to build it from the source because it will not only be compiled with your machine's specs in mind, but it will also work a lot better as far as themes and fonts go. Once you do that, the plugins for Mozilla, Epiphany, Galeon, Firefox, and about any other browser go into /usr/lib/nsbrowser/plugins.
Check your gcc version (I think gcc -v) and make sure your system is compiled with a compatible version. See that gcc32 in the plugin path? If you're not using a gcc version 3.2 or later, you may have trouble. If that is the case, try linking to one of the other plugin versions. There should be two or three to choose from.