Rollover noise can GENERALLY be improved by running the correct oil, and not that Syntrans crap. Having said that, if rollover and backlash are excessive the box was not shimmed up correctly when re-assembled here in Australia. This is an easy fix. If the box has to come out it is worth contemplating fitting 0.74 ratio 5th gear while it is apart.
To isolate whether it is gearbox or diff, try it in fourth gear. All the clunk you get in fourth gear is diff, if you get more in other gears, that extra portion of it is gearbox. The diffs are very easy to fix, they need to be opened up and the tolerances closed in. It is a combination of crown wheel to pinion backlash and hemisphere slop, and they generally get worse after about 2000km from new. Commodores have the same hemisphere slop, but not the C&P backlash.
If you're not driving a manual you're really just steering.