I fitted a high ratio (1:1) LT230R about a year ago and it's a lot noisier than the high mileage LT230T it replaced.

There's a whine that almost sounds like a turbo whistle, but there's also a grumble type noise and vibration which I can feel through my feet.
Below 100km/h they're barely noticable, but above they get much louder much faster.

The box was supposed to have done only 80,000km and from the condition of the insides I believe it. I pulled the gear cover and checked all the gear teeth, they're all in excellent condition and there's minimal backlash in the diff.

If I knock the gearbox into neutral the grumbling stays, but if I knock the transfer into neutral it goes quiet. Does this indicate input/intermediate gears or can this also be a driveshaft rumble which stops when the load is removed from the drive end?

It'll be a while before it comes out again, unless of course the noise gets worse.
Driveshaft unis are all in good condition, two replaced in the last two years. Slip joints have a bit of wear which could be throwing them out of balance.