I had a similar issue with mine/ still have, just over a year ago I had 5thgear synchro go, so the entire gearbox was replaced under warranty, I also paid the extra to change the clutch whilst the box was out, I still have the bearing noise and the rattles, just seems to be the norm, the noise you hear at the rear of the box could be due to the vibration travelling through the gear box itself,
If its now out of warranty id say "If it aint broke dont fix it"