JOA v3 has been uploaded, this will hopefully be the last major update. After at least 3 years in the making, most major bugs have been fixed. Cutscene animations, objectives, the skating glitch on yavin swamp, shader conflicts with academy, not being able to dual wield on ns_streets and many more bugs have been fixed. Big thanks to user sanguinehipster at jkhub.org for fixing many of these bugs.
His mod can be found here: Jkhub.org
Some small bugs still remain, the Galak boss fight on doom_shields doesn't work perfectly and some shaders may still flicker, but I'd say I've probably spent enough time working on this now. Unless any major gameplay breaking bugs are found, this is the final version of my mod.