Maybe a bit late now, but worth checking that the camplate plunger moves freely and has a spring that works. Plunger housing adjusted correctly, with just a couple of threads showing below the locknut as a reasonable start. Removing the plunger housing will drain off the oil, so be prepared to catch it and inspect the oil for dirt, debris, clues etc.
When you say "clunks" I assume you mean as you change gear, rather than a rhythmic sound when engaged which is more likely a broken, chipped or missing gear tooth. A rattle sounds like something loose or broken, investigate further before riding, possible locked box is dangerous.......
Swarfy.