I'm not sure I follow sorry
I think I've already isolated it to the gearbox, specifically the output/secondary shaft. I say this because changing gear doesn't change the note or volume of the sound, so changing engine speed doesn't affect it - thus its nothing to do with the engine. This is also changing the speed of the input/primary shaft (which is linked to the engine via the clutch) and also doesn't change its tone/sound either so I wouldn't expect it to be a bearing or clearance on the input shaft in the gearbox.
So that narrows it down to the output shaft of the gearbox and it's bearings and clearances, the differential, and the driveshafts/wheelbearings (a long shot)
I will do some more tests (slightly dangerous ones). If I jack one wheel off the ground, it will rotate at twice the speed through the differential as the drive from the other wheel will be passed through the spider gear, accelerating it. This will allow me to double the speed on the side gears in the diff giving them a run for their money. I will confirm this theory with actual wheel rpm with one and both off the ground (I have an optical tacho) - the shorter drive shaft side should spin a bit quicker naturally, if it doesn't or there is a significant difference that could be a clue, but the sum of the 2 wheels should equal the single wheel speed at the same rpm (I think....)
It will be difficult to compare the noise of this test to the normal driving noise since I won't have road noise, or proper engine load (I can and will log engine load as I have a gadget for that, and I can then compare that to the engine load I get at say 50mph cruising just for reference). This stationary test might just tell me if I can isolate the noise to the left or right half, at which point, I'll take a gamble and fit a re-manufactured drive shaft and change the wheel bearing while I'm there (not cheap jobs, but I can do it myself). If the problem persists (and it probably will) then I'll have to get a gearbox for it (not expensive, but costly labour having it installed). Ideally a 6 speed from the 2.0MZR if they're mechanically compatible with the existing gearbox/(new) clutch, driveshafts and control cables etc, as the gear ratios better suit my 100% stop start round town commute.