Eh? So you don't know much about what happens post-RotJ. Anyway, the Yuuzhan Vong were an enemy added in the New Jedi Order books. Controversial, but I thought that was what you were seeking.
Anyway, Legacy of War was a mod that planned to add them into the game. Seems like the idea died.
There's nothing as far as I know about the time line you seem to be asking for. In fact, the Jedi Knight series is pretty soon after RotJ. After that you get what happened during the Thrawn Trilogy (first series of Star Wars books ever written outside of the movies) but they're still using standard Rebel Alliance and Imperial ships. Then there's the Yuuzhan Vong and New Jedi Order era. You'd have to get pretty far in the future and that's an area few books or comic books have explored so a mod team would have to design a lot of things themselves.
Unfortunately, there's no such mod out there. Sorry.